Copolymers for suppression of autoimmune diseases, and methods of use

ABSTRACT

Random three- and four-amino acid copolymers having lengths of 14-, 35- and 50-amino acid residues are provided. Fifty-mers of FEAK were effective inhibitors of MBP 85-99- or proteolipid protein (PLP) 40-60-specific HLA-DR-2-restricted T cell clones. These copolymers efficiently suppressed the mouse disease EAE, which was induced in a susceptible SJL/J (H-2 s ) strain of mice with either whole spinal cord homogenate (WSCH) or with the encephalitogenic epitope PLP 139-151 (SEQ ID NO:4). YFAK 50-mer having a molar ratio of about Y 0.8:F 0.2 inhibited binding of biotinylated MBP 85-99 epitope to HLA-DR-2 molecules more efficiently than either unlabeled MBP 85-99 or Copaxone®. YFAK and FAK copolymers efficiently suppressed EAE induced in SJL/J (H-2 S ) mice with the encephalitogenic epitope PLP 139-151. Copolymers YFAK, VYAK and tryptophan-containing VWAK were efficacious in alleviating severity and duration of symptoms of EAE induced by MBP 85-99 (SEQ ID NO:2), in a humanized mouse model expressing genes for both an HLA-DR-2 linked to multiple sclerosis (MS) in humans and for a T cell receptor from an MS patient.

RELATED APPLICATIONS

This application is a continuation-in-part of PCT/US02/31,399 filed Oct.3, 2002 in the PCT Receiving Office of the U.S. Patent and TrademarkOffice, which claims priority from provisional application 60/326,705filed Oct. 3, 2001 in the U.S. Patent and Trademark Office, both ofwhich are hereby incorporated by reference in their entirety herein.

GOVERNMENT FUNDING

This invention was made in part with government support under grantCA-47554 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

TECHNICAL FIELD

The invention relates to design of copolymers having particular aminoacids in specific molar ratios, synthesized into polypeptides ofpredetermined length and capable of suppression of symptoms andfrequency of recurrent episodes of an autoimmune disease.

BACKGROUND

Multiple sclerosis (MS) is an inflammatory disease of the centralnervous system affecting 0.1% of the population, and is associated innorthern European caucasoid MS patients with the HLA-DR-2 (DRB1*1501)haplotype (Olerup, O. et al. 1991. Tissue Antigens 38:1-15). An animalmodel of MS, experimental autoimmune encephalomyelitis (EAE), is a Tcell-mediated autoimmune disease. EAE can be induced by subcutaneousinjection of peptides derived from myelin components such as myelinbasic protein (MBP; Madsen, L. S. et al. 1999. Nat. Genet. 23:343-347),proteolipid protein (PLP; Greer, J. M. et al. 1992. J. Immunol.149:783-788) or myelin oligodendrocyte glycoprotein (MOG; Mendel, I. etal. 1995. Eur. J. Immunol. 25:1951-1959).

In the course of EAE, autoreactive CD4⁺ T cells recognize self-antigenspresented by murine class II MHC molecules (e.g. H-2A^(s)), ultimatelyleading to pathological changes that can be monitored as clinical signsof disease. EAE provides a well studied system for testing the efficacyof potential therapeutic compounds to suppress the disease. Thesecompounds have included cytokines (Leonard, J. P. et al. 1996. Ann. N.Y.Acad. Sci. 795:216-226), peptide antigens that induce anergy (Gaur, A.et al. 1992. Science 258:1491-1494) or that induce oral tolerance(Kennedy, K. J. et al. 1997. J. Immunol. 159:1036-1044; Weiner, H. L.1997. Immunol. Today 18:335-343), or altered peptide ligands (Pfeiffer,C. et al. 1995. J. Exp. Med. 181:1569-1574; Nicholson, L. B. et al.1997. Proc. Natl. Acad. Sci. USA 94:9279-9284).

Copolymer 1 (Cop1; Copaxone®; YEAK) is a random amino acid copolymer ofalanine (A), lysine (K), glutamic acid (E) and tyrosine (Y) in a molarratio of approximately 5:3:1.5:1. Cop1 is synthesized in solution usingN-carboxyamino acid anhydrides (Teitelbaum D. et al. 1971. Eur. J.Immunol. 1:242-248). Initially, this and other related copolymers wereused to define the genetic basis of immune responsiveness, now known asclass II MHC genes (McDevitt, H. O., and M. Sela. 1965. J. Exp. Med.122:517-532; McDevitt, H. O., and M. Sela. 1967. J. Exp. Med.126:969-978). Cop1, also known as poly (Y,E,A,K) or YEAK was found to beeffective both in suppression of experimental allergic encephalomyelitis(Teitelbaum D. et al. 1971. Eur. J. Immunol. 1:242-248; Teitelbaum D. etal. 1973. Eur. J. Immunol. 3:273-279; Teitelbaum D, et al. 1974; Clin.Immunol. Immunopathol 3:256-262; Aharoni R. et al. 1993. Eur. J.Immunol. 23:17-25) and in the treatment of relapsing forms of multiplesclerosis (MS; Bornstein, M. B. et al. 1987. N. Engl. J. Med.317:408-414; Johnson, K. P. et al. 1995. Neurology 45:1268-1276;Johnson, K. P. et al. 1998. Neurology 50:701-708).

Cop1 has been approved as a therapy for MS and currently is in wide use.However, while Cop1 reduces the MS relapse rate, it does not eliminaterelapse, and is not curative for the disease. It is important to developimproved compositions and methods of use for treatment of MS, and forother autoimmune diseases.

SUMMARY

Certain aspects of the present invention relate to linear random aminoacid copolymers made of amino acid residues Xaa₁, Xaa₂, Ala and Lys in amolar ratio which provides a copolymer having the desired biologicalproperties recited herein. In certain preferred embodiments, the molarration of (Xaa₁+Xaa₂+K):A is in the range of 1:1 to 1:10. In certainpreferred embodiments, the molar ration of K:A is in the range of 1:1.5to 1:15. In certain preferred embodiments, the molar ration of(Xaa₁+Xaa₂):(K+A) is in the range of 1:2 to 1:20. Expressions such as“(Xaa₁+Xaa₂)” means the sum of the molar ratios of Xaa₁ and Xaa₂, etc.Xaa₁ and Xaa₂ are, independently, residues having hydrophobic sidechainsExemplary naturally occurring amino acid residues include Ala, Gly, Ile,Leu, Met, Phe, Pro, Trp, Tyr, and Val. Non-naturally occurring aminoacid analogs that can incorporated into the subject copolymers includeresidues having alkyl, alkenyl, cycloalkyl, heteroalkyl and arylsidechains. In certain preferred embodiments, the hydrophobic sidechainshave between 3 and 10 carbon atoms (in addition to the Cα carbon), andmay optionally include 1-3 heteroatoms such as O, S and N. Exemplarynaturally occurring amino acid residues with this characteristic includeIle, Leu, Met, Phe, Trp, Tyr and Val. Preferably, Xaa₁ are Xaa₂ aredifferent.

A feature of the invention is a linear random amino acid copolymer YFAKcomprising tyrosine (Y), phenylalanine (F), alanine (A) and lysine (K).In a related embodiment, a molar ratio of (Y+F):A:K has a range of about1:5:3 to about 1:10:3. The expression “(Y+F)” means the sum of the molarratios of Y and F, compared to the molar ratios of each of A and K.

The amino acids are polymerized by a solid phase reaction; in analternative embodiment, the amino acids are polymerized by solutionchemistry. In a related embodiment, the molar ratio of F to Y is about1, for example, the molar ratio of F to Y is at least about 2, or Y isabout 4.

In an alternative embodiment, the molar ratio of Y is greater than F,for example, the molar ratio of Y to F is at least about 2, or the molarratio of Y to F is at least about 4. In general, the copolymer is atleast about 25 amino acid residues in length, for example, the copolymeris at least about 35 amino acid residues, at least about 50 amino acidresidues, or at least about 70 amino acid residues in length.

In one embodiment, the invention provides a linear random amino acidcopolymer comprising Y:F:A:K in a molar ratio having a range of about0.2:0.8:5:3 to about 0.2:0.8:10:3. In a related embodiment, theinvention provides a linear random amino acid copolymer comprisingY:F:A:K in a molar ratio having a range of about 0.5:0.5:5:3 to about0.5:0.5:10:3. In another related embodiment, the invention provides alinear random amino acid copolymer comprising Y:F:A:K in a molar ratiohaving a range of about 0.8:0.2:5:3 to about 0.8:0.2:10:3. In general,the copolymer amino acids are polymerized using a solid phase reaction;alternatively, the copolymer amino acids are polymerized by solutionphase chemistry.

In another aspect, the invention provides a linear random amino acidcopolymer VFAK comprising valine (V), phenylalanine (F), alanine (A) andlysine (K). In another aspect, the invention provides a linear randomamino acid copolymer VWAK comprising valine (V), tryptophan (W), alanine(A) and lysine (K). In another aspect, the invention provides a linearrandom amino acid copolymer VYAK comprising valine (V), tyrosine (Y),alanine (A) and lysine (K). In another aspect, the invention provides alinear random amino acid copolymer FAK comprising phenylalanine (F),alanine (A) and lysine (K), in a molar ratio F:A:K having a range ofabout 1:5:3 to about 1:10:3. In another aspect, the invention provides alinear random amino acid copolymer VAK comprising valine (V), alanine(A) and lysine (K) in a molar ratio V:A:K having a range of about 1:5:3to about 1:10:3. In another aspect, the invention provides a linearrandom amino acid copolymer WAK comprising tryptophan (W), alanine (A)and lysine (K) in a molar ratio W:A:K having a range of about 1:5:3 toabout 1:10:3. In another aspect, the invention provides a linear randomamino acid copolymer VWAK comprising valine (V), tryptophan (W), alanine(A) and lysine (K), in a molar ratio (V+W):A:K having a range of about1:5:3 to about 1:10:3. The expression “(V+W)” means the sum of the molarratios of V and W, compared to the molar ratios of each of A and K.

In another aspect, the invention provides a linear random amino acidcopolymer VWAK comprising valine (V), tryptophan (W), alanine (A) andlysine (K). In a related embodiment, a molar ratio V:W:A:K having arange of about 0.5:0.5:5:3 to about 0.5:0.5:10:3. In another aspect, theinvention provides a linear random amino acid copolymer VEAK comprisingvaline (V), glutamic acid (E), alanine (A) and lysine (K). In a relatedembodiment, V:E:A:K has a molar ratio in the range of about 1:1.5:5:3 toabout 1:1.5:10:3. In another aspect, the invention provides a linearrandom amino acid copolymer FEAK comprising phenylalanine (F), glutamicacid (E), alanine (A) and lysine (K). In a related embodiment, F:E:A:Khas a molar ratio in the range of about 1:1.5:5:3 to about 1:1.5:10:3.In another aspect, the invention provides a linear random amino acidcopolymer VYAK comprising valine (V), tyrosine (Y), alanine (A) andlysine (K). In a related embodiment, (V+Y):A:K has a molar ratio in therange of about 1:5:3 to about 1:10:3. The expression “(V+Y)” means thesum of the molar ratios of V and Y, compared to the molar ratios of eachof A and K. In another aspect, the invention provides a linear randomamino acid copolymer VYAK comprising valine (V), tyrosine (Y), alanine(A) and lysine (K). In a related embodiment, V:Y:A:K has a molar ratioof about 0.5:0.5:5:3 to about 0.5:0.5:10:3. Further, any of thecompositions provided here may be provided in a pharmaceuticallyacceptable buffer, and/or in a unit dosage.

1. The featured copolymers herein are comprised of amino acids asdescribed, and are further considered to be equivalent to copolymerssharing the amino acid compositions as described and also containing oneor more additional substituents, for example, have one or moreadditional amino acids, such that the resulting copolymer has about thesame function. For example, a copolymer FEAK, FAK, VWAK, VYAK, YFAK, orany of the copolymer compositions as provided herein, which is comprisedsubstantially of this composition, i.e, is at least about 60%, or atleast about 70%, or at least about 80%, or at least about 90%, or atleast about 95% or about 99% the composition provided herein, and hasabout the same functional properties as a copolymer provided herein, isconsidered equivalent to the composition as provided herein. Thefunction is considered to be about the same if a dosage of a compositionherein that is effective for treating an autoimmune disease is about thesame as a dosage of a copolymer comprising substantially the samesubstitutents as a composition herein, for treating the autoimmunedisease. The copolymers herein can further comprise a modification whichis at least one non-peptide bond. The non-peptide bond can be selectedfrom the group consisting of: —CH₂NH—, —CH₂S—, —CH₂CH₂—, —CH═CH—,—COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. For example, the non-peptide bond is—CH₂NH— or —CH═CH—.

The featured copolymer compositions herein can be combined with at leastone additional therapeutic agent. In related embodiments, the additionaltherapeutic agent is an antibody, an enzyme inhibitor, an antibacterial,an antiviral, a steroid, a nonsteroidal anti-inflammatory, anantimetabolite, a cytokine, a cytokine blocking agent, an adhesionmolecule blocking agent or a soluble cytokine receptor. For example, thecytokine is selected from the group consisting of β-interferon,interleukin-4 and interleukin-10.

An embodiment of the invention is a kit comprising at least one unitdosage of a copolymer described above.

2. A feature of the invention is a method of manufacture of acomposition for use in treating a subject having an autoimmune disease,wherein the composition comprises any of random linear amino acidcopolymers FAK, YFAK, VYAK, VWAK, VEAK and FEAK. In general, thecopolymer has a length of at least about 50 residues, for example, atleast about 70 residues. Further, in such a use, the composition furthercomprises a pharmaceutically acceptable carrier. Further, the use caninvolve administering the composition in an effective dose. An“effective dose” is an amount of the composition that remediates eitheror both of clinical symptoms and frequency of recurrence of anautoimmune disease. Prior to administering, the copolymer is selectedfor inhibiting binding of an autoantigenic peptide to an MHC class IIprotein associated with the autoimmune disease. For example, thecopolymer that inhibits a class II-specific T cell response to an MHCclass II protein-peptide complex is selected. The autoimmune disease isselected from the group consisting of Hashimoto's thyroiditis;idiopathic myxedema, a severe hypothyroidism; multiple sclerosis, ademyelinating disease; myasthenia gravis; Guillain-Barre syndrome;systemic lupus erythematosis; uveitis; autoimmune oophoritis; chronicimmune thrombocytopenic purpura; colitis; diabetes; Grave's disease;psoriasis; pemphigus vulgaris; and rheumatoid arthritis, and others. Ina preferred embodiment, the autoimmune disease is multiple sclerosis;the autoimmune disease is rheumatoid arthritis; or the autoimmunedisease is diabetes. An additional therapeutic agent, can beco-administered, for example, the additional therapeutic agent is anantibody, an enzyme inhibitor, an antibacterial agent, an antiviralagent, a steroid, a nonsteroidal anti-inflammatory agent, anantimetabolite, a cytokine, a cytokine blocking agent, an adhesionmolecule blocking agent, or a soluble cytokine receptor. The cytokineis: interferon-β, interleukin-4, or interleukin-10. The enzyme inhibitoris a protease inhibitor or a cyclooxygenase inhibitor. The copolymersused in the methods herein can further comprise a modification which isat least one non-peptide bond. The non-peptide bond can be selected fromthe group consisting of: —CH₂NH—, —CH₂S—, —CH₂CH₂—, —CH═CH—, —COCH₂—,—CH(OH)CH₂—, and —CH₂SO—. For example, the non-peptide bond is —CH₂NH—or —CH═CH—.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a set of panels of graphs showing inhibition ofHLA-DR-2-restricted MBP 84-102-specific T cell lines 2E12 (FIG. 1A),8073 (FIG. 1B) and Hy1B (FIG. 1C), in the presence of the randomcopolymers. Irradiated L466 (FIG. 1A) or MGAR (FIGS. 1B, 1C) cells wereco-incubated in duplicate with MBP 85-99 (SEQ ID NO: 2) at a finalconcentration of 4 μM (A) or 12.5 μM (FIGS. 1B, 1C) and differentconcentrations of each of the random copolymers as indicated for 2 hr at37° C., then T cells were added and incubated for 24 hr at 37° C.Supernatants (30 μl) were incubated with IL-2-dependent cytolytic T-celllymphocytes (CTLL), followed by labeling with ³H-thymidine (1 μCi/well)for 12 hr.

FIG. 2 is a set of line graphs (FIG. 2A) showing inhibition ofHLA-DR-2-restricted PLP 40-60-specific human T cells 106 A, and a set ofbar graphs (FIGS. 2B and 2C) showing inhibition of H-2^(s)-restrictedPLP 139-151-specific mouse T cell hybridomas (hPLP/1 and hPLP/c4,respectively), in the presence of random copolymers. Irradiated L466(FIG. 2A) or splenocytes from SJL/J (FIGS. 2B and 2C) mice wereco-incubated with the proteolipid protein peptide PLP 40-60 (SEQ ID NO:3) at a final concentration of 60 μM (A) and the concentrations ofdifferent copolymers as indicated on the abscissa, or with PLP 139-151peptide (SEQ ID NO: 4; in B and C) at the final concentration of 24 μM,and the different copolymers (28 μM) for 2 hr at 37° C., then T cellswere added and incubated for 24 hr at 37° C. Supernatants (30 μl) wereincubated with IL-2-dependent CTLL, followed by labeling with³H-thymidine (1 μCi/well) for 12 hr. * indicates 0% inhibition.

FIG. 3 is a set of graphs showing suppression by different randomcopolymers VEAK, FEAK, and Copaxone®, of EAE induced with PLP 139-151(SEQ ID NO: 4) peptide. SJL/J mice were co-injected subcutaneously with50 μg of PLP 139-151 (SEQ ID NO: 4) peptide and 500 μg of the indicatedrandom copolymers, or with PLP 139-151 (SEQ ID NO: 4) alone. Progressionof the disease was monitored for the appearance of clinical symptoms,scored on the ordinate, for the days shown on the abscissa. Resultsshown on the ordinate represent the mean daily score of clinicalsymptoms.

FIG. 4 is a graph showing inhibition of binding of biotinylated MBP86-100 (SEQ ID NO: 1) to HLA-DR-2 molecules by random copolymers FAK,YFAK (0.8:0.2), YFAK (0.2:0.8), YFAK (0.5:0.5), and Cop 1. Recombinantwater-soluble HLA-DR-2 molecules were incubated with biotinylated MBP86-100 (SEQ ID NO: 1; 0.13 μM) and with the unlabeled random copolymersor the synthetic unlabeled peptide control MBP 85-99 (SEQ ID NO: 2), atconcentrations shown on the abscissa. Incubations were carried out induplicate at pH 7.0 for 40 hr at 37° C. Results shown as inhibition ofbinding on the ordinate represent one out of two independentexperiments. Specific binding is expressed as percentage of inhibitionusing the formula: percentage of inhibition=100%−[(absorbance at 410 nmwith competitor−background)/absorbance withoutcompetitor−background)×100]. The signals at 410 nm without competitorwere 0.8-0.9 and the background was 0.1.

FIG. 5 is a set of graphs showing inhibition of HLA-DR-2-restricted MBP84-102-specific T cells for each of cell lines 2E12, 8073 and Hy1B, inthe presence of random copolymers FAK, YFAK (0.8:0.2), YFAK (0.2:0.8),YFAK (0.5:0.5), and Cop 1. Irradiated MGAR cells were co-incubated induplicates with MBP 85-99 (SEQ ID NO: 2) at the final concentration of12.5 μM and different concentrations of the random copolymers for 2 hrat 37° C., then T cells were added and incubated for 24 hr at 37° C.Supernatants (30 μl) were incubated with each of the IL-2-dependent CTLLcell lines as indicated, and were labeled with ³H-thymidine (1 μCi/well)for 12 hr.

FIG. 6 is a set of graphs showing suppression by different randomcopolymers FAK, YFAK 0.2:0.8, YFAK 0.8:0.2, YFAK 0.5:0.5, or Copaxone®of EAE induced with PLP 139-151 (SEQ ID NO: 4) peptide. SJL/J mice wereco-injected subcutaneously with 50 μg of PLP 139-151 (SEQ ID NO: 4)peptide and 500 μg of the indicated random copolymers, or immunized withPLP 139-151 (SEQ ID NO: 4) alone. Progression of the disease wasmonitored for the appearance of clinical symptoms for the days afterdisease induction shown on the abscissa. FIG. 6A shows the results ofthe mean daily score of clinical symptoms as shown on the ordinate foreach group of five to nine mice per group in each of two experiments.FIG. 6B shows data for each individual mouse, with the copolymertreatment of the group listed at the top of each column, and the maximalclinical score observed for the mouse indicated in the upper right handcorner of each box, for a representative experiment.

FIG. 7 is a set of line graphs showing suppression, by different randomcopolymers YFAK, VWAK, VWAK, or Cop 1, of EAE induced with MBP 85-89(SEQ ID NO: 2) peptide, and control mice not treated with copolymer.Humanized mice (Madsen, L. S. et al. 1999 Nat. Genet. 23(3): 343-347;and D. Altman, D. Hafler, and V. Kuchroo, unpublished) carry transgenesHLA DR-2 (DRA*0101 and DRB1*1501) and TCR from MS patient Ob, which is aV(D)J rearrangement of TCRα and TCRβ amplified from clone Ob.1A12.Co-immunized mice were co-injected on day 0 with 500 μg of the copolymeror control material as indicated, and 50 μg of the EAE inducing peptideMBP 85-89 (SEQ ID NO: 2). Pre-immunized mice were preinjected with thecopolymer two days prior to EAE induction. The copolymers VYAK and VWAKrespectively, have molar ratios of 0.5:0.5:5:3 of V:Y:A:K and ofV:W:A:K, respectively. The data points indicate progression of thedisease by scoring of clinical symptoms, on the ordinate, on each ofdays 3, 5, 7, 9, 11, 14, 16, 18, 22, 25, 28, 32, 37, 40, 43 and 50, onthe abscissa.

FIG. 8 is a set of line graphs, replotted together from data for threeof the groups of animals from FIG. 7: diamonds are control EAE-inducedmice not further receiving copolymer treatment; squares are EAE-inducedmice treated with YFAK 0.5:0.5; and triangles are EAE-induced micetreated with Cop1. Each treatment in this figure was administered twodays prior to EAE induction, i.e., vaccination against disease.

DESCRIPTION OF SPECIFIC EMBODIMENTS

Unless the context otherwise requires, as used in this description andin the following claims, the terms below shall have the meanings as setforth:

The term “autoimmune condition” or “autoimmune disease” means a diseasestate caused by an inappropriate immune response that is directed to aself-encoded entity which is known as an autoantigen. The copolymercompounds provided herein can be used to treat symptoms of an autoimmunedisease, a class of disorder which includes Hashimoto's thyroiditis;idiopathic myxedema, a severe hypothyroidism; multiple sclerosis, ademyelinating disease marked by patches or hardened tissue in the brainor the spinal cord; myasthenia gravis which is a disease havingprogressive weakness of muscles caused by autoimmune attack onacetylcholine receptors at neuromuscular junctions; Guillain-Barresyndrome, a polyneuritis; systemic lupus erythematosis; uveitis;autoimmune oophoritis; chronic immune thrombocytopenic purpura; colitis;diabetes; Grave's disease, which is a form of hypothyroidism; psoriasis;pemphigus vulgaris; and rheumatoid arthritis (RA).

The term “demyelinating condition” includes a disease state in which aportion of the myelin sheath, consisting of plasma membrane wrappedaround the elongated portion of the nerve cell, is removed bydegradation. A demyelinating condition can arise post-vaccination,post-anti TNF treatment, post-viral infection, and in MS.

The term “derivative” of an amino acid means a chemically related formof that amino acid having an additional substituent, for example,N-carboxyanhydride group, a γ-benzyl group, an ε,N-trifluoroacetylgroup, or a halide group attached to an atom of the amino acid.

The term “analog” means a chemically related form of that amino acidhaving a different configuration, for example, an isomer, or aD-configuration rather than an L-configuration, or an organic moleculewith the approximate size, charge, and shape of the amino acid, or anamino acid with modification to the atoms that are involved in thepeptide bond, so that the copolymer having the analog residue is moreprotease resistant than an otherwise similar copolymer lacking suchanalog, whether the analog is interior or is located at a terminus ofthe copolymer, compared to the copolymer without the analog.

The phrases “amino acid” and “amino acid copolymer” can include one ormore components which are amino acid derivatives and/or amino acidanalogs as defined herein, the derivative or analog comprising part orthe entirety of the residues for any one or more of the 20 naturallyoccurring amino acids indicated by that composition. For example, in anamino acid copolymer composition having one or more tyrosine residues, aportion of one or more of those residues can be substituted withhomotyrosine. Further, an amino acid copolymer having one or morenon-peptide or peptidomimetic bonds between two adjacent residues, isincluded within this definition.

The term “hydrophobic” amino acid means aliphatic amino acids alanine(A, or ala), glycine (G, or gly), isoleucine (I, or ile), leucine (L, orleu), methionine (M, or met), proline (P, or pro), and valine (V, orval), the terms in parentheses being the one letter and three letterstandard code abbreviations for each amino acid, and aromatic aminoacids tryptophan (W, or trp), phenylalanine (F, or phe), and tyrosine(Y, or tyr). These amino acids confer hydrophobicity as a function ofthe length of aliphatic and size of aromatic side chains, when found asresidues within a copolymer or other polypeptide.

The term “charged” amino acid means amino acids aspartic acid (D orasp), glutamic acid (E or glu), arginine (R or arg) and lysine (K orlys), which confer a positive (lys, and arg) or negative (asp, glu)charge at physiological values of pH on an aqueous solution of acopolymer or other amino acid composition containing one or moreresidues of these amino acids. Histidine (H or his) is hydrophobic at pH7, and charged at pH 6.

The term “anergy” means unresponsiveness of the immune system of asubject to an antigen.

The term “subject” as used herein indicates a mammal, including a human.

The term “heterologous cell” means a cell for production of an MHCprotein which is unrelated to a cell of a subject, e.g., theheterologous cell is not a cell of a mammal. The heterologous cell forexample can be from a cold blooded animal, for example, from aninvertebrate; the heterologous cell is an insect cell, or a cell of amicroorganism such as a yeast cell.

The term “surfaces of Class II MHC HLA-DR-2 protein” includes theportions of the protein molecule in its three-dimensional configurationwhich are in contact with its external environment, including thosefeatures of the protein that interact with aqueous solvent and arecapable of binding to other cell components such as nucleic acids, otherproteins, and peptides.

The terms “P1 pocket” and “P4 pocket” include three dimensionalpolymorphic regions on the peptide binding surface of the Class II MHCprotein molecule that accommodate amino acid residue side chains from apeptide that is bound to the Class II MHC protein (Fridkis-Hareli, M. etal. 1998. J. Immunol. 160:4386-4397; Fridkis-Hareli, M. et. al. 2000.Human Immunol. 61:640; Fridkis-Hareli, M. et al. 2001. Human Immunol.62:753-763), including a bound naturally occurring antigen or epitope,and a bound synthetic peptide or copolymer.

The terms “P-1 position” and “P5 position” refer to amino acid residueson the Class II MHC protein molecule peptide complex which directlycontact the T-cell receptor (Fridkis-Hareli, M. et. al. 2000. HumanImmunol. 61:640; Fridkis-Hareli, M. et al. 2001. Human Immunol.62:753-763). The P-1 position refers to the amino acid which precedesthe amino acid residue of the peptide that occupies the P1 pocket. TheP5 position refers to the amino acid residue that follows the amino acidresidue that occupies the P4 pocket.

The term “antigen binding groove” refers to a three dimensional antigeninteractive site on the surface of the Class II MHC protein molecule(Stern, L. J. et. al., Nature 368:215 (1994)) that is formed by surfacesof both the α and β subunits of the Class II MHC protein molecule.

The term “pharmaceutically acceptable carrier” includes any and allsolvents, dispersion media, coatings, antimicrobials such asantibacterial and antifungal agents, isotonic and absorption delayingagents and the like that are physiologically compatible. Preferably, thecarrier is suitable for intravenous, intramuscular, oral,intraperitoneal, transdermal, or subcutaneous administration, and theactive compound can be coated in a material to protect it frominactivation by the action of acids or other adverse natural conditions.

An autoimmune disease results when a host's immune response fails todistinguish foreign antigens from self molecules (autoantigens) therebyeliciting an aberrant immune response. The immune response towards selfmolecules in an autoimmune disease results in a deviation from thenormal state of self-tolerance, which involves the destruction of Tcells and B cells capable of reacting against autoantigens, which hasbeen prevented by events that occur in the development of the immunesystem early in life. The cell surface proteins that play a central rolein regulation of immune responses through their ability to bind andpresent processed peptides to T cells are the major histocompatibilitycomplex (MHC) molecules (Rothbard, J. B. et al., Annu. Rev. Immunol.9:527 (1991)).

In addition to MS, other demyelinating conditions have been found tooccur, for example, post-viral infection, post-vaccination,post-encephalomyelitis (Wucherpfennig K. W. et al. 1991. Immunol. Today12:277-282) and following administration of certain anti-TNF agents (FDATalk Paper, Food and Drug Administration Public Health Service,Rockville, Md., http://www.fda.gov/bbs/topics/ANSWERS/ANSDO954.html).

Copolymers of Amino Acids as Therapeutic Agents for Autoimmune Diseases

Methods of the invention include use of a class of agents that can bindto Class II

MHC proteins encoded by particular alleles. Such an agent can bind to aparticular Class II MHC protein, and thus inhibit and/or prevent thebinding of an autoantigen involved in an autoimmune disease, or uponbinding can induce anergy, so that there is no response of the immunesystem to the autoantigen.

A number of therapeutic agents have been developed to treat autoimmunediseases. For example, agents have been developed that can, byinhibiting a cyclooxygenase, prevent formation of low molecular weightinflammatory compounds. Also, agents are available that can function byinhibiting a protein mediator of inflammation, by sequestering theinflammatory protein tumor necrosis factor (TNF) with an anti-TNFspecific monoclonal antibody fragment, or with a soluble form of the TNFreceptor. Finally, agents are available that target and inhibit thefunction of a protein on the surface of a T cell (the CD4 receptor orthe cell adhesion receptor ICAM-1) thereby preventing a productiveinteraction with an antigen presenting cell (APC). However, compositionswhich are natural folded proteins as therapeutic agents can incurproblems in production, formulation, storage, and delivery. Further,natural proteins can be contaminated with pathogenic agents such asviruses and prions.

An additional target for inhibition of an autoimmune response is the setof lymphocyte surface proteins represented by the MHC molecules.Specifically, these proteins are encoded by the Class II MHC genesdesignated as HLA (human leukocyte antigen)-DR, -DQ and -DP. Each of theMHC genes is found in a large number of alternative or allelic formswithin a mammalian population. The genomes of subjects affected withcertain autoimmune diseases, for example, MS and rheumatoid arthritis(RA), are more likely to carry one or more characteristic Class II MHCalleles, to which that disease is linked.

A potential source of agents for treatment of MS and other demyelinatingconditions is to identify peptides that bind selectively in vitro to apurified Class II MHC allele protein molecule, particularly to a proteinwhich is a product of an Class II MHC allele associated withdemyelinating conditions. In addition, the agent should bind to thatprotein as it occurs on the surfaces of antigen presenting cells invivo, and thereby block, anergize, or inactivate the class of T cellsthat are responsible for the demyelinating condition, such as MS.

The Class II MHC protein consists of two approximately equal-sizedsubunits, α and β, which are transmembrane proteins. A peptide-bindingcleft, which is formed by protein features of both α and β subunits, isthe site of presentation of the antigen to T cells. There are at leastthree types of Class II MHC molecules: HLA-DR, -DQ, and -DP, and thereare numerous alleles of each type. The Class II MHC molecules areexpressed predominantly on the surfaces of B lymphocytes and antigenpresenting cells such as macrophages and dendritic cells (Mengle-Gaw,L., The Major Histocompatibility Complex (MHC), in the Encyclopedia ofMolecular Biology, Oxford: Blackwell Science Ltd., 1994, pp. 602-606).

An embodiment of the invention includes a novel method for treatingautoimmune diseases, by targeting Class II MHC molecules with a class ofcompounds identified as copolymers that include three or more differentamino acids.

A copolymer of the invention can be synthesized using fmoc- ortBoc-protected initiating amino acid analogs, or the like, which areimmobilized on a resin in an automated peptide synthesis apparatus forfurther polymerization (solid state synthesis). The amino acids arepolymerized in molar ratios that can be adjusted to provide a copolymerwith optimal binding characteristics.

Synthesis procedures can include providing a solution which is a mixtureof the chosen amino acids in an activated form, for example, activatedas an N-carboxy anhydride, in the appropriate molar ratios of each ofthe appropriately derivatized amino acid precursors (derivatized toprotect certain functional groups, such as the ε amino group ofL-lysine, for example the precursor ε,N-trifluoroacetyl-L-lysine).Alternatively, the synthesis procedure can involve online mixing duringthe synthetic procedure of derivatized precursors of the selected aminoacids in the preferred molar ratios. Heteropolymer synthesis servicescan be obtained commercially, for example, at Chiron Technologies,Clayton, Australia, the Harvard Medical School Biopolymer Laboratory,Boston, Mass., and at Advanced ChemTech, Inc., Louisville, Ky.

Examples of such resin supports for peptide synthesis include aMerrifield resin, chloromethylated polystyrene with 1% DVB cross-links;an fmoc amino acid Wang resin, 4-benzyloxybenzyl alcohol, the resinsbeing pre-loaded with an amino acid (for example, fmoc-D-trp(boc)-Wangresin). Resins are available in different mesh sizes, for example100-200 mesh, and high loading or low loading densities offunctionalization of the initiating amino acid.

A solution of the different derivatized amino acids to be polymerizedinto the composition of the invention, preferably protected as isconventional in peptide synthesis, is added to sample of beads e.g.,fmoc. Reagents for synthesis, for deblocking, and for cleavage of thecomplete copolymer molecules for removal from the resin are availablefrom manufacturers of the apparatus (Applied Biosystems PeptideSynthesizer, Foster City, Calif., or Advanced ChemTech, Louisville,Ky.); see e.g., M. Bodansky, Principles of Peptide Synthesis, 2nd Ed.,Springer-Verlag, 1991, the contents of which are herein incorporated byreference. Additional amino acids or analogs or derivatives of aminoacids, can be added to the at least three amino acids selected tocomprise the copolymers, to substitute for a small proportion of thoseamino acids, to provide, for example, a copolymer having increasedprotease resistance and therefore having enhanced pharmacologicalproperties such as longer in vivo lifetime. Examples of analogs arehomotyrosine, or other substituted tyrosine derivatives, andaminobutyric acid, each available as an fmoc derivative from AdvancedChemTech.

The invention in other embodiments provides copolymers havingnon-peptide bonds between one or more of the amino acid residues in thecopolymer backbone. The presence of non-peptide bonds can confer, interalia, improved pharmacological properties on the copolymer analogsincluding improved binding to Class II MHC protein, increased serumhalf-life, and/or improved bioavailability. Such copolymerpeptidomimetics can be synthesized having the same molar ratios of aminoacid precursors as a “parent” copolymer, i.e., the parent copolymerhaving peptide bonds and comprising amino acids in random sequence,however using an amino acid analog that forms a bond that is not apeptide bond. The copolymer analogs are potential therapeutic agents forautoimmune diseases, as they retain the ability of to parent copolymerto inhibit or to prevent interaction of an auto-antigenic peptide, e.g.,an auto-antigen associated with MS such as MBP 58-99 (SEQ ID No: 2), tointeract with a Class II MHC protein, for example, with Class II MHCDR-2 protein, and to prevent or cure the autoimmune disease such as EAEin mice or MS in humans.

For illustrative purposes, peptidomimetics of the present invention canbe generated using, for example, benzodiazepines (e.g., see Freidingeret al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOMPublisher: Leiden, Netherlands, 1988), substituted gama lactam rings(Garvey et al. in Peptides: Chemistry and Biology, G. R. Marshall ed.,ESCOM Publisher: Leiden, Netherlands, 1988, p123), C-7 mimics (Huffmanet al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOMPublisher: Leiden, Netherlands, 1988, p. 105), keto-methylenepseudopeptides (Ewenson et al. (1986) J Med Chem 29:295; and Ewenson etal. in Peptides: Structure and Function (Proceedings of the 9th AmericanPeptide Symposium) Pierce Chemical Co. Rockland, Ill., 1985), β-turndipeptide cores (Nagai et al. (1985) Tetrahedron Lett 26:647; and Satoet al. (1986) J Chem Soc Perkin Trans 1:1231), β-aminoalcohols (Gordonet al. (1985) Biochem Biophys Res Commun 126:419; and Dann et al. (1986)Biochem Biophys Res Commun 134:71), diaminoketones (Natarajan et al.(1984) Biochem Biophys Res Commun 124:141), and methyleneamino-modified(Roark et al. in Peptides: Chemistry and Biology, G. R. Marshall ed.,ESCOM Publisher: Leiden, Netherlands, 1988, p134). Also, see generally,Session III: Analytic and synthetic methods, in Peptides: Chemistry andBiology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands,1988).

In addition, the present invention specifically contemplates the use ofconformationally restrained mimics of peptide secondary structure.Numerous surrogates have been developed for the amide bond of peptides.Frequently exploited surrogates for the amide bond include the followinggroups (i) trans-olefins, (ii) fluoroalkene, (iii) methyleneamino, (iv)phosphonamides, and (v) sulfonamides.

Examples of Surrogates

Additionally, peptidomimietics based on more substantial modificationsof the backbone of the copolymer can be used. Peptidomimetics which fallin this category include (i) retro-inverso analogs, and (ii) N-alkylglycine analogs (so-called peptoids).

Examples of Analogs

Furthermore, the methods of combinatorial chemistry are being brought tobear on the development of new peptidomimetics. For example, oneembodiment of a so-called “peptide morphing” strategy focuses on therandom generation of a library of peptide analogs that comprise a widerange of peptide bond substitutes. See, for example, PCT PublicationWO9948897; Gierasch et al. (2000) Org. Lett. 2:3999-4002; Michielin etal. (2002) J. Am. Chem. Soc. 124: 11131-11141; and Harrison et al.(2002) J. Am. Chem. Soc. 124:13352-13353.

In an exemplary embodiment, the copolymer can be derived as aretro-inverso peptidomimetic. Retro-inverso peptidomimetics can be madeaccording to the methods known in the art, such as that described by theSisto et al. U.S. Pat. No. 4,522,752. As a general guide, cites whichare most susceptible to proteolysis are typically altered, with lesssusceptible amide linkages being optional for mimetic switching Thefinal product, or intermediates thereof, can be purified by HPLC.

In another illustrative embodiment, the copolymer can be derived as aretro-enatio peptidomimetic. Retro-enantio analogs such as this can besynthesized commercially available D-amino acids (or analogs thereof)and standard solid- or solution-phase peptide-synthesis techniques.

In still another illustrative embodiment, trans-olefin derivatives canbe made for any of the subject copolymers. A trans-olefin peptidomimeticcan be synthesized according to the method of Y. K. Shue et al. (1987)Tetrahedron Letters 28:3225 and also according to other methods known inthe art. It will be appreciated that variations in the cited procedure,or other procedures available, may be necessary according to the natureof the reagent used.

Still another class of peptidomimetic derivatives include phosphonatederivatives. The synthesis of such phosphonate derivatives can beadapted from known synthesis schemes. See, for example, Loots et al. inPeptides: Chemistry and Biology, (Escom Science Publishers, Leiden,1988, p. 118); Petrillo et al. in Peptides: Structure and Function(Proceedings of the 9th American Peptide Symposium, Pierce Chemical Co.Rockland, Ill., 1985).

Many other peptidomimetic structures are known in the art and can bereadily adapted for use in the subject copolymers. To illustrate, thecopolymer may incorporate the 1-azabicyclo[4.3.0]nonane surrogate (seeKim et al. (1997) J. Org. Chem. 62:2847), or an N-acyl piperazic acid(see Xi et al. (1998) J. Am. Chem. Soc. 120:80), or a 2-substitutedpiperazine moiety as a constrained amino acid analog (see Williams etal. (1996) J. Med. Chem. 39:1345-1348). In still other embodiments,certain amino acid residues can be replaced with aryl and bi-arylmoieties, e.g., monocyclic or bicyclic aromatic or heteroaromaticnucleus, or a biaromatic, aromatic-heteroaromatic, or biheteroaromaticnucleus.

Advantages of the copolymer peptidomimetics, in comparison to thecopolymers having only peptide bonds, can include: more economicalproduction, greater chemical stability, enhanced pharmacologicalproperties (half-life, absorption, potency, efficacy, etc.), alteredspecificity (e.g., a broader or a narrower spectrum of biologicalactivities), and reduced antigenicity. Without being limited by anyparticular theory or mechanism, it is envisioned that a non-peptide bondlocated at one or both of the copolymer termini reduces or eliminatesdegradation of the copolymer analog by circulating processiveexopeptidases, and prolongs the half-life of the copolymer followingadministration to a subject.

Therapeutic Compositions in the Methods of the Invention

A pharmaceutically acceptable carrier includes any and all solvents,dispersion media, coatings, antimicrobials such as antibacterial andantifungal agents, isotonic and absorption delaying agents and the likethat are physiologically compatible. Preferably, the carrier is suitablefor intravenous, intramuscular, oral, intraperitoneal, transdermal, orsubcutaneous administration, and the active compound can be coated in amaterial to protect it from inactivation by the action of acids or otheradverse natural conditions.

The methods of the invention include incorporation of a copolymer into apharmaceutical composition suitable for administration to a subject. Acomposition of the present invention can be administered by a variety ofmethods known in the art as will be appreciated by the skilled artisan.The active compound can be prepared with carriers that will protect itagainst rapid release, such as a controlled release formulation,including implants, transdermal patches, and microencapsulated deliverysystems. Many methods for the preparation of such formulations arepatented and are generally known to those skilled in the art. See, e.g.,Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson,Ed., Marcel Dekker, Inc., NY, 1978. Therapeutic compositions fordelivery in a pharmaceutically acceptable carrier are sterile, and arepreferably stable under the conditions of manufacture and storage. Thecomposition can be formulated as a solution, microemulsion, liposome, orother ordered structure suitable to high drug concentration.

Dosage regimens can be adjusted to provide the optimum desired response(e.g., a therapeutic response). For example, a single bolus can beadministered, several divided doses can be administered over time, orthe dose can be proportionally reduced or increased as indicated by theexigencies of the disease situation.

In general, an embodiment of the invention is to administer a suitabledaily dose of a therapeutic copolymer composition that will be thelowest effective dose to produce a therapeutic effect, for example,mitigation of symptoms. The therapeutic heteropolymer compounds of theinvention are preferably administered at a dose per subject per day ofat least about 2 mg, at least about 5 mg, at least about 10 mg or atleast about 20 mg as appropriate minimal starting dosages. In general,the compound of the effective dose of the composition of the inventioncan be administered in the range of about 50 to about 400 micrograms ofthe compound per kilogram of the subject per day.

A physician or veterinarian having ordinary skill in the art can readilydetermine and prescribe the effective dose of the pharmaceuticalcomposition required. For example, the physician or veterinarian couldstart doses of the compound of the invention employed in thepharmaceutical composition at a level lower than that required in orderto achieve the desired therapeutic effect, and increase the dosage withtime until the desired effect is achieved.

In another embodiment, the pharmaceutical composition includes also anadditional therapeutic agent. Thus in a method of the invention thepharmaceutical copolymer composition can be administered as part of acombination therapy, i.e. in combination with an additional agent oragents. Examples of materials that can be used as combinationtherapeutics with the copolymers for treatment of autoimmune disease andarthritic conditions as additional therapeutic agents include: anantibody or an antibody fragment that can bind specifically to aninflammatory molecule or an unwanted cytokine such as interleukin-6,interleukin-8, granulocyte macrophage colony stimulating factor, andtumor necrosis factor-α; an enzyme inhibitor which can be a protein,such as α₁-antitrypsin, or aprotinin; an enzyme inhibitor which can be acyclooxygenase inhibitor; an engineered binding protein, for example, anengineered protein that is a protease inhibitor such an engineeredinhibitor of a kallikrein; an antibacterial agent, which can be anantibiotic such as amoxicillin, rifampicin, erythromycin; an antiviralagent, which can be a low molecular weight chemical, such as acyclovir;a steroid, for example a corticosteroid, or a sex steroid such asprogesterone; a non-steroidal anti-inflammatory agent such as aspirin,ibuprofen, or acetaminophen; an anti-cancer agent such as methotrexate,cis-platin, 5-fluorouracil, or adriamycin; a cytokine blocking agent; anadhesion molecule blocking agent; or a cytokine.

An additional therapeutic agent can be a cytokine, which as used hereinincludes without limitation agents which are naturally occurringproteins or variants and which function as growth factors, lymphokines,interferons particularly interferon-β, tumor necrosis factors,angiogenic or antiangiogenic factors, erythropoietins, thrombopoietins,interleukins, maturation factors, chemotactic proteins, or the like. Anadditional agent to be added to a copolymer of amino acids which areembodiments of the invention herein can be a different copolymer, forexample, Copaxone® which is a YEAK or Cop 1, or a copolymer comprising asubset of these or other amino acids (Aharoni et al. WO 00/05250,PCT/US99/16747), or an oligopeptide or peptide derivative (Strominger etal. WO 00/05249, PCT/US99/16617; WO 02/59143, PCT/US02/02071). Preferredtherapeutic agents to be used in combination with a composition of theinvention and which are cytokines include interferon-β, interleukin-4and interleukin-10.

A therapeutic agent to be used with the composition of the invention canbe an engineered binding protein, known to one of skill in the art ofremodeling a protein that is covalently attached to a virion coatprotein by virtue of genetic fusion (Ladner, R. et al., U.S. Pat. No.5,233,409; Ladner, R. et al., U.S. Pat. No. 5,403,484), and can be madeaccording to methods known in the art. A protein that binds any of avariety of other targets can be engineered and used in the presentinvention as a therapeutic agent in combination with a heteropolymer ofthe invention.

An improvement in the symptoms as a result of such administration isnoted by a decrease in frequency of recurrences of episodes of MS, bydecrease in severity of symptoms, and by elimination of recurrentepisodes for a period of time after the start of administration. Atherapeutically effective dosage preferably reduces symptoms andfrequency of recurrences by at least about 20%, for example, by at leastabout 40%, by at least about 60%, and by at least about 80%, or by about100% elimination of one or more symptoms, or elimination of recurrencesof the autoimmune disease, relative to untreated subjects. The period oftime can be at least about one month, at least about six months, or atleast about one year.

Methods of use of random synthetic copolymers can be the basis oftreating other autoimmune diseases which are associated with HLA-DR geneproducts, by competing with candidate autoantigens for binding to theseprotein receptor molecules, or by inducing T cell anergy or even T cellapoptosis, or by suppression of T cells, such that subsequent T cellresponse to an autoantigen is inhibited in vivo. Further, syntheticcopolymers having one or more additional components, such as amino acidanalogs or derivatives added in varying quantities into thepolymerization reaction, can be effective inhibitors of a variety ofautoimmune T cell responses.

The activity of Cop1 appears to involve, as a first step, binding to thesurface of antigen-presenting cells (APC), for example to class II MHCproteins (Fridkis-Hareli M. et al. 1994. Proc. Natl. Acad. Sci. USA91:4872-4876), following which its effectiveness may be due either tocompetition with myelin antigens (for example, MBP, PLP, MOG) foractivation of specific effector T cells recognizing peptide epitopesderived from these proteins (Ben-Nun, A. et al. 1996. J. Neurol.243:S14-22; Teitelbaum, D. et al. 1996. J. Neuroimmunol. 64:209-217),and/or induction of antigen-specific regulatory T cells (Aharoni R. etal. 1993. Eur. J. Immunol. 23:17-25).

Examination of additional copolymers and investigation of the mechanismsinvolved in their activities could potentially result in informationthat could lead to improved therapeutic reagents. Recent studies haveshown that virtually all of the large variety of copolymers found in therandom mixture of YEAK bound to purified molecules of each of humanHLA-DR1, -DR-2 and -DR4 molecules, showing that YEAK generally binds topurified class II MHC proteins (Fridkis-Hareli, M., and J. L.Strominger. 1998. J. Immunol. 160:4386-4397). Cop1 further competes forbinding of MBP 85-99 to HLA-DR-2 (DRB1*1501) and inhibits responses ofDR-2-restricted T cells to MBP 85-99. Study of the binding to class IIMHC molecules of random copolymers containing only 3 of the 4 aminoacids of Cop1, for example, YAK, revealed that YAK is the most effective(Fridkis-Hareli, M. et al. 1999. Int. Immunol. 11:635-641).

The binding motif of Cop1 to the MS-associated molecule HLA DR-2(DRB1*1501) shows E at P-2, K at P-1 and Y at P1, with no preferencesobserved at other positions (Fridkis-Hareli, M. et al. 1999. J. Immunol.162:4697-4704). Further, A is overrepresented at P1. As P1 is the anchorposition, binding of Y at this position was not anticipated. The P1pocket in proteins encoded by the DR-2 allele is small (due to thepresence of β86Val rather than β86Gly), and overrepresentation of A atthis position may result from this fact. The effect of K at P-1 appearsto be due to stabilization of binding by the interaction of K withresidues in the top of the α1 helix, similarly to residue K at P-1 of HA306-318 (SEQ ID NO:5) complexed with HLA-DR1 which can interact with theside chains of α1 helix residues at Sα53 or Eα55 (Stem, L. J. et al.1994. Nature 368:215-221).

Copolymers designed according to the binding motif of MBP 85-99(Wucherpfennig, K. W. et al. 1994. J. Exp. Med. 179:279-290) might bebetter therapeutic agents than Cop1. As provided herein, several randomthree- and four-amino acid copolymers, each synthesized as 14-, 35- and50-mers in length, were made by the solid phase method. Design of thesecopolymers was made primarily by choice of amino acids with reference tothe anchor residues of MBP 85-99 bound to HLA-DR-2 (DRB1*1501)(Wucherpfennig, K. W. et al. 1994. J. Exp. Med. 179:279-290; Smith, K.J. et al. 1998. J. Exp. Med. 19:1511-1520), particularly the P1 anchor,to improve the effectiveness of the copolymers. Effects of thesecopolymers on autoantigen-specific T cell responses in MS, and ondisease progression of EAE, an animal model of MS, are shown in theExamples below.

A major goal in the treatment of autoimmune diseases has beendevelopment of antigen-specific immunomodulating therapies thatinterfere with the trimolecular interaction of the autoreactive T cellreceptor (TCR) with the autoantigenic peptides presented by self MHCreceptors at the surface of antigen-presenting cells. Theseimmunotherapies of T cell-mediated autoimmune diseases have beensuccessful in animal models with known target antigens (see, forexample, Weiner, H. L. 1997. Immunol. Today 18:335-343; Nicholson, L. B.et al. 1997. Proc. Natl. Acad. Sci. USA 94:9279-9284). The use ofaltered peptide ligands (APL) has been used both to treat EAE(Nicholson, L. B. et al. 1997. Proc. Natl. Acad. Sci. USA 94:9279-9284;Brocke, S. et al. 1996. Nature 379:343-346) and recently to treat MS(Bielekova, B. et al. 2000. Nat. Med. 10:1167-1175; Kappos, L. et al.2000. Nat. Med. 10:1176-1182), with contradictory findings.

Cop1 (Copaxone®), an approved therapy for relapsing-remitting MS, wasproposed to act as a promiscuous binder to class II MHC molecules(Fridkis-Hareli, M., and J. L. Strominger. 1998. J. Immunol.160:4386-4397), as an antagonist of the TCR (Aharoni, R. et al., 1999.Proc. Natl. Acad. Sci. USA 96: 634-639), and/or as an inducer ofsuppressor cells (Aharoni R. et al. 1993. Eur. J. Immunol. 23:17-25).Copaxone® is currently in wide use, has shown little or no toxicity, andhas sustained efficacy in MS patients over a period of 6 years (Johnson,K. P. et al. 2000. Mult. Scler. 6:255-266). However, this agent wasfound to reduce frequency of relapse by about 30%, but did not eliminaterelapse. Development of novel compounds may provide improved therapeuticagents for MS and possibly for other autoimmune disorders.

In Examples 1-6, an optimal size of copolymers described herein wasdetermined using copolymers which are 14-, 35- or 50-mers in length.Since the 50-mers are shown herein to be most efficient in bindingHLA-DR-2 and in inhibiting MBP-specific T cell responses, the additionalcopolymers used in Examples 7-11 were all synthesized as 50-mers. A sizeof 50 amino acids or longer, found here to provide efficient inhibitionof antigen presentation and suppression of EAE, suggests that the randomcopolymers herein act by binding to and then clustering class II MHCmolecules in one portion of the cell membrane, similarly to Copaxone®(Fridkis-Hareli, M. et al. 1997 Int. Immunol. 9: 925-34) or oligomerizedT cell epitopes (Rotzschke, O. et al. 1997 Proc. Natl. Acad. Sci. USA94: 14642-14647).

The residues in the random copolymers in Examples 7-11 herein weredesigned mainly on the basis of the anchor residues of theimmunodominant T cell epitope MBP 85-99 peptide (SEQ ID NO: 2). The Y inCopolymer 1 was found in the presumed P1 pocket of the HLA DR-2(DRB1*1501) molecule (Fridkis-Hareli, M. et al. 1999 J. Immunol. 162:4697-4704), although Y may be too large for this pocket which has a goodfit with F, and accommodates V89 in MBP85-99. Moreover, the F92 in MBP85-99 (SEQ ID NO: 2) is in the P4 pocket (Smith, K. J. et al. 1998 J.Exp. Med. 19: 1511-1520), but Y or W may be a tighter fit for thispocket. The interrelationship between these two residues in the Y- andF-containing copolymers provided herein is examined using copolymerssynthesized at different ratios of Y:F. Further, V- and W-containingcopolymers and V- and Y-containing copolymers, selected for synthesis onthe basis of the need for differently sized aromatic groups toaccommodate the differing sizes of the P1 and P4 pockets, are shown inExample 11 to be particularly effective in treating EAE symptoms. Withpresent knowledge of the size, shape and charge distributions of each ofthe P1 and P4 pockets, and the data on V- and W-containing polymers astherapeutic agents for EAE, it is possible to design amino acids withnovel organic side chains that could substitute for V and W,respectively, in synthesis of a copolymer, to provide an agent having anequivalent or even tighter fit of the side chain into these sites than Vand W. A copolymer containing such a compound might be an even moreuseful therapeutic agent for an autoimmune disease such as EAE or MS.

The invention having now been fully described, additional embodiments ofthe invention can be found in the Examples and in the claims below,which embodiments are not to be construed as further limiting. Thecontents of each of the publications and patents cited are herebyincorporated in their entirety by reference herein.

EXAMPLES Materials and Methods

Copolymers, peptides and antibodies. Poly (Y,E,A,K), referred to asYEAK, poly(V,E,A,K) or VEAK; and poly(F,E,A,K) or FEAK, in molar ratiosapproximating those found in Cop1 (wherein the V or F are present in thesame molar ratio as the Y in Cop1), were synthesized by the solid phasemethod as 14-, 35- and 50-mers (Chiron Technologies, Clayton,Australia), by using fmoc amino acids mixed in the desired ratios ateach cycle. Cop1 batch 52596, in the molar ratio of 1 Y:1.5 E:4.3 A:3.3K (indicated herein as Y:E:A:K having a molar ratio of 1:1.5:4.4:3.3,with an average molecular weight (MW) of 8,150, (Teitelbaum D. et al.1971. Eur. J. Immunol. 1:242-248), was obtained from Teva PharmaceuticalIndustries (Petach Tiqva, Israel). Glatiramer acetate (Cop 1, Copaxone®)was obtained from Teva Marion Partners, Kansas City, Mo. Biotinylationof Cop1 was performed with excess N-hydroxysuccinimide biotin (Sigma) inDMSO as described (Fridkis-Hareli M. et al. 1994. Proc. Natl. Acad. Sci.USA 91:4872-4876). Unreacted biotin was removed by dialysis(Spectra/Por® membrane MWCO 500; Spectrum Medical Industries, LagunaHills, Calif.).

Peptides were synthesized using solid phase techniques (Barany, G., andR. Merrifield. 1979. Academic Press, New York, N.Y.) on an AppliedBiosystems Peptide Synthesizer and purified by reversed-phaseHPLC(RP-HPLC). Peptide sequences were MBP (human basic myelin protein)86-100, NPVVHFFKNIVTPRT (SEQ ID NO: 1); MBP 85-99, ENPVVHFFKNIVTPR (SEQID NO: 2), MW 1795; PLP (human proteolipid protein) 40-60,TGTEKLIETYFSKNYQDYEYL (SEQ ID NO: 3), MW 2603; and mouse PLP 139-151,HSLGKWLGHPDKF (SEQ ID NO: 4), MW 1520, either unlabeled or labeled withbiotin linked to the N-terminus by the spacer SGSG and free acid at theC-terminus.

Copolymers FAK (molar ratio 1:5:3), YFAK (molar ratio 0.2:0.8:5:3), YFAK(molar ratio 0.8:0.2:5:3) and YFAK (molar ratio 0.5:0.5:5:3) weresynthesized by solid phase chemistry as 50-mers (Chiron Technologies,Clayton, Australia). A variance of about 10% from the input molar ratiosand observed the amino acid compositions of the resulting polymers wasfound consistent with previously reported data from use of thisprocedure. Equivalent embodiments of the copolymers described herein canhave molar ratios that vary about two-fold, about three-fold or aboutfour-fold from those specified herein without substantial loss ofpharmacological properties. Molar ratios that are about two-fold, aboutthree-fold or about four-fold different from those used in the Examples,which merely illustrate the present invention and are not furtherlimiting, are within the embodiments of the invention herein.

Protein expression and purification. Soluble HLA-DR-2 molecules wereexpressed in Drosophila S2 cells and purified as described (Kalandadze,A. et al. 1996. J. Biol. Chem. 271:20156-20162). Cells were grown at 26°C. in roller bottles in ExCell 401 medium (JRH Biosciences, Lenexa,Kans.) supplemented with 0-5% fetal bovine serum (Sigma Chemicals, St.Louis, Mo.). Cells were harvested 4-5 days after induction by 1 mMCuSO₄. Supernatant from harvested cells was sequentially passed throughProtein A, Protein G and Protein A-LB3.1 columns, followed by elution ofthe bound HLA-DR with 50 mM 3-[cyclohexylamino]-1-propanesulfonic acid(CAPS), pH 11.5, and neutralized with 200 mM phosphate (pH 6.0).Proteins were concentrated on a Centriprep 10 membrane (Amicon, Beverly,Mass.).

HPLC separation and microsequencing. Different copolymers were separatedand pool sequenced as previously described (Fridkis-Hareli, M. et al.1999. J. Immunol. 162:4697-4704). Briefly, the fractionation was bymicrobore HPLC using a Zorbax C₁₈ 1.0 mm reverse-phase column on aHewlett-Packard 1090 HPLC with 1040 diode array detector. Copolymerswere eluted at a flow rate of 54 μl/min with a gradient of 0.055%trifluoroacetic acid (TFA) in acetonitrile (0% at 0 to 10 min, 33% at 73min and 60% at 105 min) Strategies for peak selection, reverse phaseseparation and Edman microsequencing have been previously described(Chicz, R. M. et al. 1993. J. Exp Med. 178: 27-47). Pooled fractionswere submitted to automated Edman degradation on a Hewlett-PackardG1005A (Palo Alto, Calif.) protein sequencer using the manufacturer'sRoutine 3.5.

Assays for Peptide Binding to Class II MHC Proteins.

(A). Solutions. The solutions used in this assay are the following:binding buffer is 20 mM 2-[N-morpholino]ethanesulfonic acid (MES), 140mM NaCl, 0.05% NaN₃, pH 5.0, unless otherwise specified; PBS is 150 mMsodium chloride, 7.5 mM sodium phosphate, dibasic, 2.5 mM sodiumphosphate, monobasic, pH 7.2; TBS is 137 mM sodium chloride, 25 mM TrispH 8.0, 2.7 mM potassium chloride; TTBS is TBS plus 0.05% Tween-20.(B). Microtiter assay plate preparation. Immunoassay plates (96-wellmicrotiter, PRO-BIND™, Falcon, Lincoln Park, N.J.) were coated with 1μg/well affinity-purified LB3.1 monoclonal antibodies in PBS (100 μltotal) for 18 hrs at 4° C. The wells were then blocked with TBS/3% BSAfor 1 hr at 37° C. and washed three times with TTBS. Before sampleaddition, 500 of TBS/1% BSA was added to each well.(C). Inhibition reactions. Biotinylated peptide MBP 86-100 (SEQ ID NO:1), final concentration 0.13 μM in 50 μl of the binding buffer, wasco-incubated with unlabeled inhibitors (random copolymers or MBP 85-99,SEQ ID NO: 2), and HLA-DR-2 molecules for 40 hr at 37° C.(D). Detection of class II MHC protein/peptide complexes. Boundpeptide-biotin was detected using streptavidin-conjugated alkalinephosphatase, as follows. Plates were washed three times with TTBS andincubated with 100 μl of streptavidin-conjugated alkaline phosphatase(1:3000, BioRad, Richmond, Calif.) for 1 hr at 37° C., followed byaddition of p-nitrophenyl phosphate in triethanolamine buffer (BioRad).Absorbance at 410 nm was monitored by a microplate reader (model MR4000;Dynatech, Chantilly, Va.).

Antigen presentation assays. HLA-DR-2-restricted T cells were MBP84-102-specific transfectants carrying the genes for TCR obtained frompatients with relapsing-remitting MS carrying DR-2 (8073, patient Ob(DRB1*1501) and Hy1B, patient Hy (DRB1*1602)), into BW 58 TCR α⁻/β⁻cells (Fridkis-Hareli, M. et al. 2001 Human Immunol. 62: 753-763); andMBP 84-102-specific (2E12) and PLP 40-60-specific (106A) hybridomas fromHLA-DR-2-transgenic mice (Madsen, L. S. et al. 1999. Nat. Genet.23:343-347). Mouse T cell hybridomas were PLP 139-151-specificH-2^(s)-restricted (hPLP/1 and hPLP/c4, Santambrogio, L. et al. 1993. J.Immunol. 151: 1116). Antigen presenting cells (APC) were L466 (L cellstransfected with HLA-DR-2b (DRB1*1501)), L416 (L cells transfected withHLA-DR-2a (DRB5*0101)), MGAR (EBV-transformed B cells homozygous forDRB1*1501), and splenocytes from SJL/J (H-2^(s)) mice. T cellstimulation experiments were performed in a total volume of 200 μl in96-well microtiter plates. Irradiated (3000 rad) APC (2.5×10⁴/well) wereco-incubated with MBP 85-99 (SEQ ID NO: 2), PLP 40-60 (SEQ ID NO: 3) orPLP 139-151 (SEQ ID NO: 4) and the random copolymers, at concentrationsindicated, for 2 hr at 37° C. Then T cells (5×10⁴/well) were added, andplates were incubated for 24 hr at 37° C. Supernatants (30 μl) weretaken and were incubated with IL-2-dependent CTLL (5×10⁴/well) for 12hr, followed by labeling with ³H-thymidine (1 μCi/well) for 12 hr.Plates were harvested, and the radioactivity was monitored using a 1450microbeta Plus liquid scintillation counter (Wallac, Gaithersburg, Md.).

Mouse strains. SJL/J (H-2^(s)) mice (8-12 weeks of age) were purchasedfrom Jackson Laboratories (Bar Harbor, Me.) and were maintained in theanimal facility at Harvard University according to the Guidelines of theCommittee on Animals of Harvard University and the Committee on Care andUse of Laboratory Animal Resources, National Research Counsel(Department of Health and Human Services Publication 85-23, revised1987). Humanized mice (Madsen, L. S. et al. 1999 Nat. Genet. 23(3):343-347; and D. Altman, D. Hafler, and V. Kuchroo, unpublished) carrytransgenes HLA DR-2 (DRA*0101 and DRB1*1501) and TCR from MS patient Ob,which is a V(D)J rearrangement of TCRα and TCRβ amplified from cloneOb.1A12.

Induction and suppression of EAE. Mice were injected subcutaneously bothin the base of the tail and the nape of the neck with either wholespinal cord homogenate (WSCH, 500 μg/mouse, prepared as previouslydescribed (Santambrogio, L. et al. 1993. J. Immunol. 151:1116-1127), orwith PLP 139-151 peptide (50 μg/mouse; SEQ ID NO:4) together with 400 μgMycobacterium tuberculosis H37Ra (BD Difco Laboratories, Sparks, Md.) inan emulsion containing equal parts of PBS and complete Freund's adjuvant(CFA; Sigma Chemical Co., St. Louis, Mo.). Pertussis toxin (ListBiological Laboratories, Campbell, Calif., 200 ng) was injectedintravenously into the tail one day after immunization. Mice were scoreddaily for clinical signs of EAE on a scale 1-5, according to theseverity of disease symptoms as previously described (Santambrogio, L.et al. 1993. J. Immunol. 151: 1116). For determination of suppression ofEAE, each copolymer (500 μg/mouse) was mixed and injected with theencephalitogenic emulsion as described above.

Neuropathology. For assessment of inflammation and demyelination, micewere perfused under anesthesia through the ascending aorta with 40 ml ofTrump's fixative (4% paraformaldehyde, 1% glutaraldehyde in 0.1 Mphosphate buffer, pH 7.4). Slices of the brain and spinal cord werepostfixed in cold 1% osmium tetroxide for 1 hr, were dehydrated througha graded series of solvents having increasing ethanol, and were embeddedin epoxy resin. Sections of one μm were obtained, and were stained withtoluidine blue and examined by light microscopy.

Example 1 Synthesis and Microchemical Analysis of Novel Copolymers

Random four-amino acid copolymers YEAK, VEAK, and FEAK, each of 14-, 35-and 50-mer in length, were synthesized by the solid phase method. V or Fwere chosen to be substituted for Y because of the following structuralinformation: the P1 pocket of DRB1*1501 includes β86V resulting in asmall pocket that can accommodate V or F but for which Y is too large tobe accommodated (except at high peptide concentration; Krieger, J. I. etal. 1991. J. Immunol. 146:2331-2340); the residue occurring at P1 in thebinding of MBP 85-99 (SEQ ID NO: 2) is V, and F might provide a tighterfit; and the residue occurring at P4 in MBP 85-99 is F.

To determine whether the solid phase synthesis procedure yieldedcopolymers similar in amino acid composition, distribution,hydrophobicity and size, as compared to copolymer that had previouslybeen generated only by solution chemistry, the novel compounds weresubjected to amino acid analysis, RP-HPLC separation andmicrosequencing.

Amino acid analysis revealed molar ratios of Y, V, F, E and K indifferent copolymers to be similar to the predicted ratios, except forA, the molar ration of which was increased in all the copolymers, andparticularly in the 35- and 50-mers. For example, in the 50-mer of VEAK,the molar ratios observed were 1.0 V: 2.1 E: 10.7 A: 2.9 K, as comparedwith the expected values of 1.0 V: 1.5 E: 5.0 A: 3.0 K. Separation ofthe copolymers by HPLC using an acetonitrile gradient showed a broadpeak with several smaller peaks, which spread between about 40 and about120 min elution time, similar to that of untreated Cop1 (Fridkis-Hareli,M., and J. L. Strominger 2001 Hum. Immunol. 62: 753-763). Edmansequencing of the first 10 amino acids showed constant ratios at eachcycle, similar to those found by amino acid analysis, and indicatingthat the sequences of amino acids in the copolymers were random.

Example 2 Binding of the Novel Random Copolymers to HLA-DR-2 Molecules

Cop1 and certain three amino acid random copolymers synthesized insolution using N-carboxyamino acid anhydrides (Teitelbaum D. et al.1971. Eur. J. Immunol. 1:242-248), viz., those containing three of theamino acids Y, E, A and K have been shown to bind to purified HLA-DR-2and to compete for binding with MBP 85-99 (Fridkis-Hareli, M., and J. L.Strominger. 1998 J. Immunol. 160:4386-4397; Fridkis-Hareli, M. et al.1999. Int. Immunol. 11:635-641).

To determine whether copolymers synthesized by the solid phase methodalso competed with this autoantigenic epitope for binding to HLA-DR-2,competitive binding assays were carried out with biotinylated MBP 86-100(SEQ ID NO: 1) and the unlabeled peptides and random copolymers. Bindingof biotinylated MBP 86-100 (SEQ ID NO: 1) to HLA-DR-2 molecules wasinhibited most efficiently by the 50-mers of YEAK, the unlabeled MBP85-99 (SEQ ID NO: 2) peptide or by Cop1. All other random copolymerstested here, i.e., those of 14 and 35 amino acid residues in length,were less effective in this assay.

Example 3 Proliferative Responses of MBP-Specific T Cells in thePresence of the Random Copolymers

A series of proliferation assays was performed to determine biologicalactivity of each of the random copolymers with several MBP84-102-specific T cell clones (see Materials and Methods).

Three types of APC, each expressing HLA-DR-2 molecules, were tested todetermine which one presented the MBP 85-99 (SEQ ID NO: 2) peptide mostefficiently. Higher levels of proliferation were observed when thispeptide was presented by the human B cell line MGAR [DR-2b(DRB1*1501)-expressing] than by L466 (DR-2b-expressing L celltransfectant) cells. When L416 [DR-2a (DRB5*0101)-expressing L cells]were used, no response was detected, confirming that all the T cellclones were restricted to the DR-2b (DRB1*1501) allele. Therefore, MGARcells, or sometimes L466 cells, were subsequently used in the antigenpresentation assays described below.

The inhibition of proliferation in the presence of different copolymersof three different T cell clones by the MBP 85-99 peptide was examined.Generally, 14-mers were not inhibitory, regardless of the T cell clonetested, whereas 35- and 50-mers showed higher levels of inhibition. Forall clones, YEAK 50-mer was approximately equivalent to Cop1 (which onaverage is a 70-mer) Inhibition fell off markedly with the YEAK 35-mer,and was very low with the YEAK 14-mer.

Inhibition of proliferation of the 2E12 T cell clone was efficient inthe presence of the 35- and 50-mers of FEAK, and in the presence of Cop1(FIG. 1A, lower left panel). VEAK did not inhibit the 2E12 clone (FIG.1A, lower right panel). The 50-mer of FEAK was somewhat less inhibitorythan Cop1. In the case of the Hy1B clone, Cop1 was the best inhibitor,and lower levels of inhibition by the 50-mers of FEAK and VEAK wereobserved (FIG. 1C).

The combination of V, E, A and K resulted in a low affinity binding toHLA-DR-2 molecules and low levels of inhibition of HLA-DR-2-restrictedMBP 85-99-specific T cells. This is in despite the observation that inthe MBP 85-99/HLA-DR-2 complex, V is the anchor residue at position 89of the peptide (SEQ ID NO: 2), interacting with β86Val in the P1 pocketof the HLA-DR-2 protein (Smith, K. J. et al. 1998. J. Exp. Med.19:1511-1520). The F side chain also fits in the P4 pocket, thus makingthe FEAK a better binding agent. Residue A may interact with the P1pocket and Y with the P4 pocket (Smith, K. J. et al. 1998. J. Exp. Med.19:1511-1520). MBP 85-99 (SEQ ID NO: 2) may be a relatively low affinitypeptide because of V89.

Residue K in FEAK is most likely important for the interaction with theTCR, similarly to K at position 93 of MBP 85-99 (SEQ ID NO: 2;Wucherpfennig, K. W. et al. 1994. J. Exp. Med. 179:279-290; Smith, K. J.et al. 1998. J. Exp. Med. 19:1511-1520). On the other hand, K locatednear the N-terminus of the copolymer in the binding site may contributeto stable interactions with the HLA-DR molecules and the TCR, similarlyto residue K at P-1 of HA 306-318 (SEQ ID NO: 5) bound to HLA-DR1 whichcan interact with the side chains of al helix residues at Sα53 or Eα55(Stern, L. J. et al. 1994. Nature 368:215-221).

Example 4 Proliferation of PLP-Specific T Cell Clones

To determine whether the random copolymers were able to inhibit thepresentation of another potential autoantigen in MS, namely PLP, twodifferent PLP epitopes were employed: human PLP 40-60 (SEQ ID NO: 3)that binds to DRB1*1501 (Krogsgaard, M. et al. 2000. J. Exp. Med.191:1395-1412), and mouse PLP 139-151 (SEQ ID NO: 4) peptide that bindsto H-2^(s) and is encephalitogenic in SJL/J mice (Tuohy, V. K. et al.1989 J. Immunol. 142:1523-1527). The T cells used in this assay were106A (PLP 40-60-specific hybridomas from HLA-DR-2-transgenic mice;Madsen, L. S. et al. 1999. Nat. Genet. 23:343-347), and hPLP/1 andhPLP/c4 (PLP 139-151-specific H-2^(s)-restricted hybridomas from SJL/Jmice; Santambrogio, L. et al. 1993. J. Immunol. 151:1116-1127).Proliferation of the T cell hybridomas was induced by the correspondingpeptides in a dose-dependent manner. Each of the different copolymerswas then added to the antigen presentation assay.

Presentation of the PLP 40-60 (SEQ ID NO: 3) epitope by the L466 APC tothe 106A T cells was inhibited most efficiently by the 35- and 50-mersof FEAK (FIG. 2A, bottom panel). The levels of inhibition were somewhathigher than in the presence of Cop1. As in the case of the MBP-specificT cells, the YEAK 50-mer approximated Cop1 (FIG. 2A, top panel), whileVEAK inhibited PLP 40-60-specific T cells only at the highestconcentrations (FIG. 2A, middle panel).

Proliferation of mouse H-2^(s)-restricted PLP 139-151-specific T cellhybridoma hPLP/1 was best inhibited by Cop1. FEAK or VEAK were somewhatless effective (FIG. 2B). The hPLP/c4 hybridoma was best inhibited bythe 50-mers of FEAK and Cop1 (FIG. 2C).

Without being limited by any particular theory, several mechanisms havebeen postulated by which the copolymers may suppress a self-reactive Tcell response: MHC/TCR blockage, competition, anergy induction,apoptosis, and bystander suppression. The first two mechanisms imply aneffect of the copolymers on the early phase of the induction phase, whenautoreactive T cells start expanding in number. Bystander suppressionmay act both on the induction and the effector phases, to promotedevelopment of regulatory T cells, or expansion of cross-reactive Tcells and thereby suppress self-reactive encephalitogenic T cells.During ex-vivo proliferation, T cells of mice immunized with PLP 139-151(SEQ ID NO: 4) developed a response only to the immunizing peptide,without any cross-reactivity to the tested copolymers. However when PLP139-151 T cells were challenged in vitro in the presence both of theself-peptides and the copolymer, the response of the T cells to PLP139-151 (SEQ ID NO: 4) was strongly abolished. Also, in severalco-immunized mice, T cells proliferated in response to PLP139-151 (SEQID NO: 4) as well as to the copolymers.

The copolymers which when administered in vivo show greatest suppressionof EAE in Examples below are also the best in suppressing T cellproliferative response to PLP 139-151 (SEQ ID NO: 4) in vitro. In suchlight, it appears that the more likely mechanism of action of thecopolymers is blockage of MHC, and competition for antigen presentation.

Example 5 In Vivo Effect of VEAK and FEAK Random Copolymers on EAEInduced by WSCH

To find out whether VEAK and FEAK random copolymers affected theclinical course of EAE in SJL/J mice, a number of in vivo experimentswere performed. The protocol for disease induction was subcutaneousinjection to co-immunize with both WSCH (500 μg) and each copolymer (500μg), similar to the protocol of previous studies of suppression of EAEby Cop1 (Teitelbaum, D. et al. 1996. J. Neuroimmunol. 64:209-217).Following disease induction, mice were observed daily for 40 days forappearance of typical clinical signs of EAE (Table 1).

The data show that mice injected with WSCH developed EAE at around day14-15 (Table 1, line 1) and had a maximal clinical score of about 2.2(incidence: 18/32, mortality: 3%). Co-immunization with 35- or 50-merVEAK (Table 1, lines 6 and 4, respectively) did not significantly affectthe course of EAE, and resulted in an incidence and maximal scoresimilar to the group injected with only WSCH, although in theseco-immunized mice the onset of the disease may have been slightlydelayed.

In contrast, mice treated with either 35-mer or 50-mer of FEAK (Table 1,lines 7 and 5 respectively) did not even develop symptoms of EAE.Treatment with Copaxone® (Table 1, line 2) suppressed EAE. One out offourteen of the mice treated with Copaxone® developed the disease on day20, with a maximal score of 3.0. Similarly, two out of sixteen miceinjected with the 50-mer of YEAK (Table 1, line 3) developed mild EAE onday 14, with a maximal score of 1.0.

To determine the extent of inflammation and demyelination in miceinjected with each of the different copolymers, central nervous systemimmunohistochemistry was performed on spinal cord samples. Samples fromthe lumbar cord of diseased mice injected with WSCH only, or with WSCHand VEAK 50-mer, showed extensive submeningeal, perivascular andparenchymal infiltration, as well as demyelination. In contrast, nosymptoms of infiltration or demyelination were detected in samples fromthose mice that had not developed any signs of disease after treatmentwith the other copolymers.

Among different random copolymers synthesized and characterized inexamples herein, FEAK was most efficient in suppression of EAE inducedby WSCH.

Example 6 Treatment with VEAK or FEAK Random Copolymers of EAE Inducedby PLP 139-151 Peptide (SEQ ID NO: 4).

To find out whether random copolymers provided herein might affectdevelopment of chronic-relapsing EAE, mice were injected subcutaneouslywith 50 μg of PLP 139-151 (SEQ ID NO: 4; the encephalitogenic epitope inthe SJL/J strain) alone, or with 50 μg of PLP 139-151 (SEQ ID NO: 4) and500 μg of the copolymer. Mice were examined on a daily basis for 90 daysafter the induction of the disease.

Immunization with the PLP 139-151 (SEQ ID NO: 4) epitope alone in CFAresulted in EAE with more severe clinical signs (FIG. 3A) compared toEAE induced by WSCH (Table 1). For example, five of eight mice developedsevere symptoms of EAE with a mortality of 33%. The first attackoccurred at about day 14 after immunization, with a maximal clinicalscore of 4.0, followed by subsequent fluctuation in disease attackspeaking approximately at days 30, 50, 70 and 85.

Co-injection with the various copolymers differentially reduced theclinical signs of EAE. In the VEAK 50-mer-treated group (FIG. 3B), fourout of eight mice showed clinical signs of EAE (mortality: 12%). Thefirst attack developed on day 13 and peaked at about day 20 (meanmaximal score: 1.6).

Co-injection with the FEAK 50-mer (FIG. 3C) resulted in three sick miceout of eight (mortality: 0%). The first attack was delayed and was lesssymptomatically severe (days 23-25, mean maximal score of 1.1) comparedto the control receiving the peptide alone, or to the VEAK-treatedgroup. Clinical symptoms were almost entirely remediated by about day40.

Treatment with Copaxone® (FIG. 3D) led to delay of the first attack(starting on day 26, peak at day 34, maximal mean score: 1.25),similarly to results obtained with FEAK. In the Copaxone® group, two outof eight mice developed EAE with a mortality of 12%.

The data in Table 1 and FIG. 3 indicate that EAE induced by either WSCHor by PLP 139-151 (SEQ ID NO: 4) peptide was efficiently suppressed bythe FEAK 50-mers. Further, these data demonstrate that 50-mers of FEAKsuppressed EAE induced by either WSCH or the PLP 139-151 (SEQ ID NO: 4)peptide more efficiently than Cop1. This observation was evident whenboth the encephalitogenic material and the copolymer were injectedsimultaneously into SJL/J mice. Cop1 inhibits EAE induced by either WSCHor the synthetic PLP peptides, and interferes with PLP-specific T cellresponses only when mice were co-immunized with both antigens(Teitelbaum, D. et al. 1996. J. Neuroimmunol. 64:209-217), suggestingthat they compete for binding to class II MHC molecules.

Without being limited by any particular theory, the mechanism ofactivity of the 50-mer random copolymers provided herein might besimilar to that of Cop1, leading to inhibition of binding of potentialautoantigenic peptides to class II MHC proteins, and subsequent T cellsuppression.

Example 7 Synthesis and Microchemical Analysis of Y- and F-ContainingCopolymers

It is shown supra that 50-mers compared to 14- or 35-mers of randomcopolymers composed of the amino acids Y, E, A and K are potentinhibitors of the binding of human immunodominant epitopes MBP 85-99(SEQ ID NO: 2) to MS-associated HLA-DR-2 (DRB1*1501). Some of thesecopolymers inhibited the response of HLA DR-2-restricted MBP84-102-specific T cells, and also suppressed EAE in the susceptibleSJL/J strain induced by the encephalitogenic epitope PLP 139-151 (SEQ IDNO: 4).

Here, analysis of each of amino acid composition and amino acid ratioswithin the copolymers, is shown for random three-copolymer FAK 50-mer,and for the four-amino acid copolymer YFAK, at different ratios of Y:F(the “Y- and F-containing” polymers), each 50-mer copolymer synthesizedas a 50-mer by the solid phase method. Amino acids that comprise thesecopolymers were chosen according to the anchor residues of the MBP 85-99(SEQ ID NO: 2) epitope bound to HLA-DR-2 (DRB1*1501) molecules.

Copolymers having different ratios of Y and F were designed according tothe following structural criteria: the P1 pocket of DRB1*1501 includesβ86V resulting in a small pocket that can accommodate F but for which Yis too large to be accommodated; thus F would provide a tighter fit forP1 although the residue occurring at P1 in the binding of MBP 85-99 isV; and the residue occurring at P4 in MBP 85-99 is F, but this pocket islarge enough to accommodate Y, which may be a better fit than F. Todetermine whether the synthesis procedure yielded substances similar inamino acid composition, distribution, hydrophobicity and size, ascompared to those generated by previous techniques, the novel compoundswere subjected to amino acid analysis, RP-HPLC separation andmicrosequencing.

Amino acid analysis revealed that the molar ratios of Y, F and K in eachof the different copolymers were similar to the expected input molarratios, except for A, the molar ratio of which was increased in all thecopolymers. HPLC separation of the copolymers, using an acetonitrilegradient as previously described for Cop1 (Fridkis-Hareli, M. et al.(1999) J. Immunol. 162, 4697-4704), showed a broad peak with severalsmaller peaks, which eluted between about 40 and 80 min, similar toelution of untreated Cop1.

Pool sequencing of the first several amino acids of each copolymersynthesized here showed random patterns, with significantly higherlevels of A over the levels of each of Y, F, or K, which corresponded tothe initially higher molar ratio of A found by analyzing the compositionof these random copolymers. No sequence specificity or preferentialpositioning of any amino acid in the copolymers was observed, indicatingthat the polymers were of random sequence.

Example 8 Binding of the Y- and F-Containing Random Copolymers toHLA-DR-2 Molecules

To determine whether the Y- and F-containing copolymers synthesizedherein by the solid phase method can compete with autoantigenicMS-associated epitope MBP 85-99 (SEQ ID NO: 2) for binding to HLA-DR-2molecules, competitive binding assays were carried out with biotinylatedMBP 86-100 (SEQ ID NO: 1) and each of the unlabeled random copolymers.

Binding of biotinylated MBP 86-100 (SEQ ID NO: 1) to HLA-DR-2 moleculeswas efficiently inhibited by FAK 50-mer and the YFAK 50-mer copolymer(having the molar ratio Y0.8:F0.2; FIG. 4). Thus, the Y- andF-containing 50-mer random copolymers herein compete with the MS-relatedepitope (SEQ ID NO: 1) for binding to MS-associated HLA-DR-2 molecules.

Example 9 Proliferative Responses of MBP-Specific T Cells in thePresence of the Random 50-mer Copolymers

Effects of the presence of each of 50-mer copolymers FAK, YFAK(0.2:0.8), YFAK (0.5:0.5), and YFAK (0.8:0.2) on proliferation of threedifferent T cell clones, in response to the MBP 85-99 (SEQ ID NO: 2)peptide, were examined, and results from two independent experiments areshown in FIG. 5.

The data show that for each of three MBP-specific HLA-DR-2-restrictedclones, the three Y- and F-containing YFAK copolymers and the FAKcopolymer were efficient inhibitors. Among these copolymers, YFAK0.2:0.8, YFAK 0.5:0.5, and FAK were better inhibitors than YFAK 0.8:0.2,and were superior to Cop 1.

The superior inhibitor activities of the three YFAK copolymers havingdifferent Y:F ratios and of the FAK copolymer were observed at lowerconcentrations (e.g., at about 20 μM) of each of these better inhibitorsfor clone 2E12, and at several low copolymer concentrations with theother T cell clones. At higher concentrations, e.g., greater than about100 μM, the observed levels of inhibition were similar for all of thecopolymers tested in this example (FIG. 5).

Example 10 Treatment of EAE Induced by PLP 139-151 (SEQ ID NO: 4) withY- and F-Containing Copolymers

In vivo experiments were carried out to determine whether the Y- andF-containing 50-mer random copolymers would affect the clinical courseof EAE in SJL/J mice. As in Examples above, the protocol forco-immunization was subcutaneous injection of SJL/J mice with, in thisexample, the encephalitogenic epitope PLP 139-151 (SEQ ID NO: 4; 50 μg)and a copolymer preparation (500 μg). Following disease induction, micewere observed daily for appearance of typical signs of EAE, during aperiod of 70 days.

Immunization with PLP 139-151 (SEQ ID NO: 4) epitope alone in CFAresulted in chronic-relapsing EAE (FIG. 6; Table 2). All 13 micereceiving this treatment developed severe EAE, with a mortality of 77%.The first signs appeared around day 11, followed by subsequentfluctuation in disease attacks, with a mean maximal score of 4.6 (FIG.6).

Co-injection of random copolymers herein differentially reduced theclinical signs of EAE. In the YFAK 0.2:0.8-treated group, only two outof 16 mice showed clinical signs of EAE (mortality: 6%), and theseclinical signs occurred with a delay in the first attack which occurredabout day 37 (mean maximal score: 0.6; FIG. 6, Table 2) rather than day11 as in the untreated group.

Similarly, in the YFAK 0.5:0.5-treated group, one sick mouse of 16 wasobserved (mortality: 0%), with the first attack developing on day 33.Further, of mice treated with YFAK 0.8:0.2, eight of 17 developed EAE,with no mortality. In this group, the observed mean maximal clinicalscore of 1.5 and the time of onset (day 27) were each indicative of aless therapeutic benefit than these data obtained for mice treated withthe YFAK preparations having the lower ratios of Y to F shown above.

Co-injection with FAK resulted in three sick mice of 17, with 12%mortality, mean maximal score of 0.9 and mean onset of day 25 (Table 2,line 5). Copaxone® co-injected with PLP 139-151 (SEQ ID NO: 4), resultedin 12 of 16 mice developing EAE, with mean onset at day 22, and a meanclinical score of 2.6 (Table 2, line 6).

Observation of clinical symptoms in individual mice in anotherexperiment (FIG. 6B) shows that YFAK 0.5:0.5 treatment eliminated allsymptoms in the entire group of mice treated with this copolymer. Fromthese data on individual mice, it is clear that F-containing copolymersare more effective in remediation of PLP-induced EAE than Cop 1, andthat a greater molar ratio of F to Y is associated with superiorremediation of EAE.

In summary, EAE induced by PLP 139-151 (SEQ ID NO: 4) was efficientlysuppressed by the three different YFAK copolymers and by FAK, with theorder of efficacy being YFAK 0.5:0.5>YFAK 0.2:0.8>FAK>YFAK 0.8:0.2. TheF-containing copolymers remediated PLP-induced EAE more effectively thanCop 1.

The Y- and F-containing random amino acid copolymers synthesized andanalyzed herein are more potent in binding to HLA-DR-2 molecules,inhibition of autoantigen-specific T cells, and suppression of EAE, thanCop 1 (Copaxone®). These copolymers were designed and synthesized mainlybased on those residues of immunodominant T cell epitope MBP 85-99 (SEQID NO:2) interacting with the MS-associated HLA-DR-2 (DRB1*1501)molecules. The length of the copolymer preparations is shown herein tobe important for activity, with the 50-mers being most efficient. Longerpolypeptides may be able to link adjacent class II molecules.

The 50-mer random copolymer FAK and the YFAK 50-mer copolymers ofdifferent molar ratios of Y to F herein are more potent than controlCopaxone® in the following functional activities: binding to HLA-DR-2molecules, inhibition of MBP-specific DR-2-restricted T cells, andsuppression of EAE. Random copolymer VEAK showed low affinity binding toHLA-DR-2 molecules, low levels of inhibition of HLA-DR-2-restricted MBP85-99-specific T cells and no effect on progression of EAE, in spite ofhaving an amino acid residue V at a position that is equivalent to theP1 of the MBP 85-99 auto antigen (SEQ ID NO: 2). Data herein show thatsubstitution of V by F resulted in a better inhibitory compound,probably due to a tighter fit of F into the P1 pocket, and Y into the P4pocket.

Most significant is the effect of the copolymers herein on progressionof EAE induced by encephalitogenic epitope PLP 139-151 (SEQ ID NO: 4).Clinical signs of EAE were significantly reduced by treatment with theYFAK copolymers or with FAK, when the encephalitogenic material and thecopolymer were injected simultaneously into SJL/J mice.

Without being limited by any particular theory, these data support amechanism of activity of the random copolymers involving the copolymersas efficient blockers of antigen presentation by class II MHC molecules,leading to inhibition of binding of the potential autoantigenic peptidesand subsequent autoimmune T cell suppression.

The YFAK 50-mer and FAK 50-mer copolymers are candidates for use intreatment of MS, a disease in which 60% of the patients are of HLA-DR-2(DRB1*1501) haplotype. Given the promiscuous binding abilities of randomcopolymers (Fridkis-Hareli, M., et al. 1998J. Immunol. 160: 4386-4397;Fridkis-Hareli, M. et al. 1999 Int. Immunol: 635-641), the copolymersherein may be beneficial also in MS patients having other HLA-DRspecificities, and might provide new therapeutic compounds for use inother autoimmune conditions.

Example 11 Co/Pre-Immunization Treatment with Valine (V)- and Tyrosine(Y)- or Valine (V)- and Tryptophan-(W)-Containing Copolymers SuppressesMBP 85-99 (SEQ ID NO: 2) Induced EAE in Humanized Mice

The peptide-binding pockets of HLA-DR-2 DRB1*1501 have a β86 Val residueat P1, and is of a size that can accommodate a residue which is a V orF, but not of sufficient size to accommodate a Y or W. In contrast, thelarge hydrophobic pocket P4 contains a β71 Ala, therefore it canaccommodate a residue of large size such as Y or W; and the P9 pocket ispromiscuous. Based on these structural considerations, copolymerscontaining valine (V) and tyrosine (Y), or valine (V) and tryptophan(W), along with A and K, were synthesized and tested for effect onprogression and symptoms of EAE induced by MBP 85-99 (SEQ ID NO: 2).

Experimental animals were humanized mice carrying transgenes HLA DR-2(DRA*0101 and DRB1*1501) and TCR from MS patient Ob, which is a V(D)Jrearrangement of TCRα and TCRβ, amplified from clone Ob.1A12. Mice ineach group were injected with MBP 85-99 (SEQ ID NO: 2) subcutaneously toinduce EAE. As shown in FIG. 7, groups of mice were pre-immunized with asingle injection two days prior to EAE induction, either with Cop1, YFAK0.5:0.5, or control MBP 85-89, or were simultaneously co-immunized withCop1, YFAK 0.5:0.5, YFAK 0.2:0.8, VYAK 0.5:0.5, or with VWAK 0.5:0.5,and with the EAE-inducing MBP 85-99 (SEQ ID NO: 2). Clinical symptomswere monitored over a course of 50 days on days indicated.

Mice in the control group that were induced with MBP 85-99 (SEQ ID NO:2) and otherwise untreated showed a severity of symptoms that exceeded aclinical score of 4 at about day 25. Clinical symptoms in this groupgenerally rose to a high level of 3-4 for eight time points (days 11 to32), prior to stabilizing at a level of severity between 2 and 3.Duration of symptoms was observed over a total of 14 time points(corresponding to day 7 to the end of the observation period, day 50),with symptoms stabilizing at between 2 and 3 in severity.

In contrast, mice induced with MBP 85-99 (SEQ ID NO: 2) and co-immunizedwith VWAK showed minimal EAE clinical symptoms (FIG. 7). During the 50day course of the experiment, the mice exhibited a return to a normalclinical appearance by day 37. The symptoms recorded for VWAK-treatedmice that appeared at about day 9 were observed at a greatest clinicalscore of about or less than about 1. Other copolymers shown in FIG. 7,while providing some symptom remediation compared to the MBP 85-99 (SEQID NO: 2) control, did not so substantially reduce the severity ofsymptoms, which ranged from 1 to slightly above 2 (for the groupco-immunized with YFAK 0.2:0.8), 1 to 2 (for the group pre-immunizedwith YFAK 0.5:0.5), and slightly greater than 1 (for the group coimmunized with YFAK 0.5:0.5).

The greatest remediation of symptoms was found in the group that wasco-immunized with VWAK, and the shortest duration of symptoms was foundin the group that was pre-immunized with YFAK 0.5:0.5. In the lattergroup, symptoms were observed for a total of only five time points,followed by disappearance of clinical symptoms. The YFAK 0.5:0.5pre-treatment data are co-plotted in FIG. 8 (square symbols) to show thecontrasts in severity and duration of symptoms of the YFAK0.5:0.5-treated group with the control group of MBP 85-99 (SEQ ID NO: 2;diamond-shaped symbols) induced and otherwise untreated, and theCop1-treated group (FIG. 8, triangular symbols). The pre-immunizationprotocol used here is equivalent to vaccination against the autoimmunedisease EAE.

In contrast to pre-immunization with YFAK 0.5:0.5, Cop1 pre-immunizationor co-immunization in the same assay, while remediating symptoms,provided relief of symptoms to a level of a clinical score of about 2 to3 (Cop1 co-immunization), or slightly greater than 3 (Cop1pre-immunization). Further, symptoms were observed for nine time points,taken from days 7 through 37 (Cop1 co-immunization) prior to micebecoming asymptomatic, or over a period of 14 time points from days 7through 50 (Cop1 pre-immunization), with mice achieving a stable levelof symptoms of greater than about 1 in severity, rather than eliminationof symptoms as in the YFAK-treated group. These data show that YFAK0.5:0.5 is most effective in pre-immunization of animals againstdevelopment of the EAE disease condition.

These data indicate that the presence of W or F in a random copolymerwith amino acids V, A, and K may increase tightness of fit of thecopolymer into a position of the class II MHC major groove, for example,into both the P1 and the P4 position. The data show that YFAK and VWAKare promising potential therapeutic agents for MS, for demyelinatingconditions, and possibly for other autoimmune diseases.

TABLE 1 Clinical EAE Induced by WSH in Mice Injected with DifferentRandom Copolymers Copolymer Incidence^(a) Percent disease^(b) Percentmortality^(c) Maximum mean score^(d) Mean day of onset^(d) — 18/32 56 32.2 ± 1.2 14.5 ± 2.3 Copaxone ®  1/14  7 0 3.0 20.0 YEAR 50-mer  2/16 120 1.0 14.0 VEAK 50-mer  8/16 50 0 2.8 ± 0.4 18.3 ± 7.4 FEAK 50-mer  0/16 0 0 — — VEAK 35-mer 3/9 30 0 1.5 ± 0.5 19.0 ± 3.0 FEAK 35-mer  0/10  00 — — Suppression of EAE induced with WSCH by the random copolymers inSJL/J mice. Mice were coinjected with 500 μg of WSCH and differentrandom copolymers (500 μg), as described in Materials and Methods.^(a)Values represent the number of mice with clinical signs of EAE as afraction of total number of immunized mice. ^(b)Values represent thepercentage of mice with clinical signs of disease. ^(c)Values representthe percentage of mortality as referred to the total number of immunizedmice. ^(d)Values representing maximum clinical score and mean day ofonset were calculated as described in Falk, O. et al. 2000 J.Exp. Med.191:717-730.

TABLE 2 Clinical EAE Induced by PLP 139-151 in Mice Injected withDifferent Random Copolymers Percent^(b) Percent^(c) Maximum^(d) Meanday^(d) Copolymer Incidence^(a) disease mortality mean score of onset —13/13 100 77 4.6 ± 0.8 11.5 ± 1.7  YFAK 0.2:0.8  2/16  13  6 0.6 ± 1.537.5 ± 7.7  YFAK 0.5:0.5  1/16   6  0 0.2 ± 1.0 33.0 ± 0    YFAK 0.8:0.2 8/17  47  0 1.5 ± 1.7 26.6 ± 10.7 FAK  3/17  18 12 0.9 ± 1.8 25.0 ±15.0 Copaxone ® 12/16  75  6 2.6 ± 1.6 22.7 ± 7.1  Suppression of EAEinduced with PLP 139-151 epitope by the random copolymers in SJL/J mice.Mice were co-injected with 50 μg of PLP 139-151 and different randomcopolymers (500 μg), as described in Materials and Methods. ^(a)Valuesrepresent the number of mice with clinical signs of EAE as a fraction oftotal number of immunized mice. ^(b)Values represent the percentage ofmice with clinical signs of disease. ^(c)Values represent the percentageof mortality as referred to the total number of immunized mice.^(d)Values representing maximum clinical score and mean day of onsetwere calculated as described in Falk, O. et al. 2000. J.Exp.Med.191:717-730.

1-20. (canceled)
 21. A linear random copolymer VFAK comprising aminoacids valine (V), phenylalanine (F), alanine (A) and lysine (K).
 22. Alinear random copolymer VWAK comprising amino acids valine (V),tryptophan (W), alanine (A) and lysine (K).
 23. A linear randomcopolymer VYAK comprising amino acids valine (V), tyrosine (Y), alanine(A) and lysine (K).
 24. A linear random copolymer FAK comprising aminoacids phenylalanine (F), alanine (A) and lysine (K).
 25. A copolymeraccording to claim 24, wherein the amino acids are polymerized in amolar ratio F:A:K having a range of about 1:5:3 to about 1:10:3.
 26. Alinear random copolymer VAK comprising amino acids valine (V), alanine(A) and lysine (K).
 27. A copolymer according to claim 26, wherein theamino acids are polymerized in a molar ratio V:A:K having a range ofabout 1:5:3 to about 1:10:3.
 28. A linear random copolymer WAKcomprising amino acids tryptophan (W), alanine (A) and lysine (K).
 29. Acopolymer according to claim 28, wherein the amino acids are polymerizedin a molar ratio W:A:K having a range of about 1:5:3 to about 1:10:3.30. A linear random copolymer VWAK comprising amino acids valine (V),tryptophan (W), alanine (A) and lysine (K).
 31. A copolymer according toclaim 30, wherein the amino acids are polymerized in a molar ratio(V+W):A:K having a range of about 1:5:3 to about 1:10:3.
 32. A linearrandom copolymer VWAK comprising amino acids valine (V), tryptophan (W),alanine (A) and lysine (K), in a molar ratio V:W:A:K having a range ofabout 0.5:0.5:5:3 to about 0.5:0.5:10:3.
 33. (canceled)
 34. A linearrandom copolymer FEAK comprising amino acids phenylalanine (F), glutamicacid (E), alanine (A) and lysine (K), comprising F:E:A:K in a molarratio having a range of about 1:1.5:5:3 to about 1:1.5:10:3.
 35. Alinear random copolymer VYAK comprising amino acids valine (V), tyrosine(Y), alanine (A) and lysine (K), in a molar ratio (V+Y):A:K having arange of about 1:5:3 to about 1:10:3.
 36. A linear random copolymer VYAKcomprising amino acids valine (V), tyrosine (Y), alanine (A) and lysine(K), in a molar ratio V:Y:A:K having a range of about 0.5:0.5:5:3 toabout 0.5:0.5:10:3.
 37. A random linear copolymer comprising amino acidsalanine (A), lysine (K), and at least one of the group of hydrophobicamino acids consisting of: valine (V), phenylalanine (F), tryptophan(W), and tyrosine (Y), providing that the copolymer is not YAK and isnot YFAK.
 38. A copolymer according to claim 37, further comprisingglutamic acid (E).
 39. A copolymer according to claim 37 furthercomprising a modification which is at least one non-peptide bond.
 40. Acomposition comprising a copolymer according to claim 37 in combinationwith at least one additional therapeutic agent.
 41. A compositionaccording to claim 40, wherein the additional therapeutic agent isselected from the group of: an antibody, an enzyme inhibitor, anantibacterial, an antiviral, a steroid, a nonsteroidalanti-inflammatory, an antimetabolite, a cytokine, a cytokine blockingagent, an adhesion molecule blocking agent, and a soluble cytokinereceptor.
 42. A composition according to claim 41, wherein the cytokineis selected from the group consisting of β-interferon, interleukin-4 andinterleukin-10.
 43. A kit comprising at least one unit dosage of arandom linear copolymer according to claim
 37. 44. A kit according toclaim 43, wherein the molar ratio in the copolymer of the amino acidsA:K:(sum of the hydrophobic amino acids) has a range of about 5:3:1 toabout 10:3:1.
 45. A method of manufacture of a composition for use intreating a subject having an autoimmune disease, wherein the compositioncomprises any of random linear amino acid copolymers FAK, VYAK, VWAK,VEAK and FEAK.
 46. A method according to claim 45, wherein the copolymerhas a length of at least about 50 residues.
 47. A method according toclaim 45, wherein the copolymer has a length of about 70 residues.
 48. Amethod according to claim 45, wherein the composition further comprisesa pharmaceutically acceptable carrier.
 49. A method according to claim45, further comprising administering the composition copolymer in aneffective dose.
 50. A method according to claim 45, further comprisingprior to administering, selecting the copolymer for inhibiting bindingof an autoantigenic peptide to an MHC class II protein associated withthe autoimmune disease.
 51. A method according to claim 45, furthercomprising selecting the copolymer for inhibiting a class II-specificresponse of a T cell to an MHC class II protein-peptide complex.
 52. Amethod according to claim 45, wherein the autoimmune disease is selectedfrom the group consisting of Hashimoto's thyroiditis; idiopathicmyxedema; multiple sclerosis; myasthenia gravis; Guillain-Barresyndrome; systemic lupus erythematosis; uveitis; autoimmune oophoritis;chronic immune thrombocytopenic purpura; colitis; diabetes; Grave'sdisease; psoriasis; pemphigus vulgaris; and rheumatoid arthritis.
 53. Amethod according to claim 45, wherein the autoimmune disease is multiplesclerosis.
 54. A method according to claim 45, wherein the autoimmunedisease is rheumatoid arthritis.
 55. A method according to claim 45,wherein the autoimmune disease is diabetes.
 56. A method according toclaim 45, further comprising co-administering an additional therapeuticagent.
 57. A method according to claim 56, wherein the additionaltherapeutic agent is selected from the group consisting of: an antibody,an enzyme inhibitor, an antibacterial agent, an antiviral agent, asteroid, a nonsteroidal anti-inflammatory agent, an antimetabolite, acytokine, a cytokine blocking agent, an adhesion molecule blockingagent, a soluble cytokine receptor, and an additional random linearamino acid copolymer composition.
 58. A method according to claim 57,wherein the cytokine is selected from the group consisting of:interferon-β, interleukin-4 and interleukin-10.
 59. A method accordingto claim 57, wherein the enzyme inhibitor is selected from the groupconsisting of: a protease inhibitor and a cyclooxygenase inhibitor. 60.A method according to claim 45, wherein the copolymer is selected fromat least one of VYAK and VWAK.
 61. A method according to claim 60,wherein the autoimmune disease is multiple sclerosis.
 62. A methodaccording to claim 45, wherein the copolymer further comprises at leastone non-peptide bond.
 63. A method according to claim 62, wherein thenon-peptide is selected from the group consisting of: —CH₂NH—, —CH₂S—,—CH₂CH₂—, —CH═CH—, —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—.
 64. A methodaccording to claim 63, wherein the non-peptide bond is —CH₂NH— or—CH═CH—.
 65. A method for treating a subject having or susceptible tomultiple sclerosis (MS), comprising administering an amino acidcopolymer having amino acids alanine (A), lysine (K), and at least onehydrophobic amino acid consisting of phenylalanine (F), tyrosine (Y),valine (V), and tryptophan (W), with the proviso that the copolymer isnot YAK and is not YFAK, wherein administering the copolymer is reducingfrequency of recurrent episodes and severity of symptoms in the subject.66. A method according to claim 65, wherein the copolymer furtherincludes glutamic acid (E).
 67. A method according to claim 66, whereinthe copolymer comprises at least one of FAK, VYAK, VWAK, VEAK and FEAK.68. A method according to claim 65, wherein prior to administering, themethod includes providing the copolymer having amino acids in theproportion of (sum of hydrophobic):A:K in a molar ratio having a rangeof about 1:5:3 to about 1:10:3.
 69. A method according to claim 66,wherein prior to administering, the method includes providing thecopolymer having amino acids in the proportion of (sum ofhydrophobic):E:A:K in a molar ratio having a range of about 1:1.5:5:3 toabout 1:1.5:10:3.
 70. A method according to claim 66, wherein thecopolymer is selected from at least one of VYAK and VWAK.
 71. A methodaccording to claim 66, wherein the copolymer further comprises at leastone non-peptide bond.
 72. A method according to claim 71, wherein thenon-peptide is selected from the group consisting of: —CH₂NH—, —CH₂S—,—CH₂CH₂—, —CH═CH—, —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—.
 73. A methodaccording to claim 71, wherein the non-peptide bond is —CH₂NH— or—CH═CH—.
 74. The method of claim 66, further comprising formulating thecopolymer in an effective dose.
 75. A linear random copolymer comprisingamino acid residues Xaa₁, Xaa₂, Ala and Lys, wherein Xaa₁ and Xaa₂ are,independently, residues having hydrophobic side chains.